diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e3ebdb859319a..de4c6687fbc0f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -65,11 +65,7 @@ repos:
     rev: 1.6.1
     hooks:
     -   id: cpplint
-        # We don't lint all C files because we don't want to lint any that are built
-        # from Cython files nor do we want to lint C files that we didn't modify for
-        # this particular codebase (e.g. src/headers, src/klib). However,
-        # we can lint all header files since they aren't "generated" like C files are.
-        exclude: ^pandas/_libs/src/(klib|headers)/
+        exclude: ^pandas/_libs/include/pandas/vendored/klib
         args: [
             --quiet,
             '--extensions=c,h',
diff --git a/MANIFEST.in b/MANIFEST.in
index 361cd8ff9ec22..781a72fdb5481 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -57,6 +57,4 @@ prune pandas/tests/io/parser/data
 
 # Selectively re-add *.cxx files that were excluded above
 graft pandas/_libs/src
-graft pandas/_libs/tslibs/src
-include pandas/_libs/pd_parser.h
-include pandas/_libs/pd_parser.c
+graft pandas/_libs/include
diff --git a/pandas/_libs/tslibs/src/datetime/date_conversions.h b/pandas/_libs/include/pandas/datetime/date_conversions.h
similarity index 100%
rename from pandas/_libs/tslibs/src/datetime/date_conversions.h
rename to pandas/_libs/include/pandas/datetime/date_conversions.h
diff --git a/pandas/_libs/tslibs/src/datetime/pd_datetime.h b/pandas/_libs/include/pandas/datetime/pd_datetime.h
similarity index 97%
rename from pandas/_libs/tslibs/src/datetime/pd_datetime.h
rename to pandas/_libs/include/pandas/datetime/pd_datetime.h
index 4e3baf4b47ed0..55aa046cf076b 100644
--- a/pandas/_libs/tslibs/src/datetime/pd_datetime.h
+++ b/pandas/_libs/include/pandas/datetime/pd_datetime.h
@@ -22,9 +22,9 @@ See NUMPY_LICENSE.txt for the license.
 #endif  // NPY_NO_DEPRECATED_API
 
 #include <numpy/ndarraytypes.h>
-#include "np_datetime.h"
-#include "np_datetime_strings.h"
-#include "date_conversions.h"
+#include "pandas/vendored/numpy/datetime/np_datetime.h"
+#include "pandas/vendored/numpy/datetime/np_datetime_strings.h"
+#include "pandas/datetime/date_conversions.h"
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/pandas/_libs/src/inline_helper.h b/pandas/_libs/include/pandas/inline_helper.h
similarity index 100%
rename from pandas/_libs/src/inline_helper.h
rename to pandas/_libs/include/pandas/inline_helper.h
diff --git a/pandas/_libs/src/parser/io.h b/pandas/_libs/include/pandas/parser/io.h
similarity index 100%
rename from pandas/_libs/src/parser/io.h
rename to pandas/_libs/include/pandas/parser/io.h
diff --git a/pandas/_libs/pd_parser.h b/pandas/_libs/include/pandas/parser/pd_parser.h
similarity index 99%
rename from pandas/_libs/pd_parser.h
rename to pandas/_libs/include/pandas/parser/pd_parser.h
index 72254090c0056..1ea94fde593ef 100644
--- a/pandas/_libs/pd_parser.h
+++ b/pandas/_libs/include/pandas/parser/pd_parser.h
@@ -14,7 +14,7 @@ extern "C" {
 
 #define PY_SSIZE_T_CLEAN
 #include <Python.h>
-#include "src/parser/tokenizer.h"
+#include "pandas/parser/tokenizer.h"
 
 typedef struct {
   int (*to_double)(char *, double *, char, char, int *);
diff --git a/pandas/_libs/src/parser/tokenizer.h b/pandas/_libs/include/pandas/parser/tokenizer.h
similarity index 98%
rename from pandas/_libs/src/parser/tokenizer.h
rename to pandas/_libs/include/pandas/parser/tokenizer.h
index 7e8c3d102ac63..a53d09012116d 100644
--- a/pandas/_libs/src/parser/tokenizer.h
+++ b/pandas/_libs/include/pandas/parser/tokenizer.h
@@ -19,10 +19,10 @@ See LICENSE for the license
 #define ERROR_INVALID_CHARS 3
 
 #include <stdint.h>
-#include "../inline_helper.h"
-#include "../headers/portable.h"
+#include "pandas/inline_helper.h"
+#include "pandas/portable.h"
 
-#include "khash.h"
+#include "pandas/vendored/klib/khash.h"
 
 #define STREAM_INIT_SIZE 32
 
diff --git a/pandas/_libs/src/headers/portable.h b/pandas/_libs/include/pandas/portable.h
similarity index 67%
rename from pandas/_libs/src/headers/portable.h
rename to pandas/_libs/include/pandas/portable.h
index a34f833b7fd6b..954b5c3cce082 100644
--- a/pandas/_libs/src/headers/portable.h
+++ b/pandas/_libs/include/pandas/portable.h
@@ -1,9 +1,18 @@
+/*
+Copyright (c) 2016, PyData Development Team
+All rights reserved.
+
+Distributed under the terms of the BSD Simplified License.
+
+The full license is in the LICENSE file, distributed with this software.
+*/
+
 #pragma once
 
 #include <string.h>
 
 #if defined(_MSC_VER)
-#define strcasecmp( s1, s2 ) _stricmp( s1, s2 )
+#define strcasecmp(s1, s2) _stricmp(s1, s2)
 #endif
 
 // GH-23516 - works around locale perf issues
diff --git a/pandas/_libs/src/skiplist.h b/pandas/_libs/include/pandas/skiplist.h
similarity index 99%
rename from pandas/_libs/src/skiplist.h
rename to pandas/_libs/include/pandas/skiplist.h
index d94099da5890e..3be9e51f42e09 100644
--- a/pandas/_libs/src/skiplist.h
+++ b/pandas/_libs/include/pandas/skiplist.h
@@ -19,7 +19,7 @@ Python recipe (https://rhettinger.wordpress.com/2010/02/06/lost-knowledge/)
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include "inline_helper.h"
+#include "pandas/inline_helper.h"
 
 PANDAS_INLINE float __skiplist_nanf(void) {
     const union {
diff --git a/pandas/_libs/src/klib/khash.h b/pandas/_libs/include/pandas/vendored/klib/khash.h
similarity index 99%
rename from pandas/_libs/src/klib/khash.h
rename to pandas/_libs/include/pandas/vendored/klib/khash.h
index e17d82d51f0fb..95b25d053a9df 100644
--- a/pandas/_libs/src/klib/khash.h
+++ b/pandas/_libs/include/pandas/vendored/klib/khash.h
@@ -112,7 +112,7 @@ int main() {
 #include <stdlib.h>
 #include <string.h>
 #include <limits.h>
-#include "../inline_helper.h"
+#include "pandas/inline_helper.h"
 
 
 // hooks for memory allocator, C-runtime allocator used per default
diff --git a/pandas/_libs/src/klib/khash_python.h b/pandas/_libs/include/pandas/vendored/klib/khash_python.h
similarity index 100%
rename from pandas/_libs/src/klib/khash_python.h
rename to pandas/_libs/include/pandas/vendored/klib/khash_python.h
diff --git a/pandas/_libs/tslibs/src/datetime/np_datetime.h b/pandas/_libs/include/pandas/vendored/numpy/datetime/np_datetime.h
similarity index 100%
rename from pandas/_libs/tslibs/src/datetime/np_datetime.h
rename to pandas/_libs/include/pandas/vendored/numpy/datetime/np_datetime.h
diff --git a/pandas/_libs/tslibs/src/datetime/np_datetime_strings.h b/pandas/_libs/include/pandas/vendored/numpy/datetime/np_datetime_strings.h
similarity index 100%
rename from pandas/_libs/tslibs/src/datetime/np_datetime_strings.h
rename to pandas/_libs/include/pandas/vendored/numpy/datetime/np_datetime_strings.h
diff --git a/pandas/_libs/src/ujson/lib/ultrajson.h b/pandas/_libs/include/pandas/vendored/ujson/lib/ultrajson.h
similarity index 99%
rename from pandas/_libs/src/ujson/lib/ultrajson.h
rename to pandas/_libs/include/pandas/vendored/ujson/lib/ultrajson.h
index d359cf27ff7e2..54bcca9e4136c 100644
--- a/pandas/_libs/src/ujson/lib/ultrajson.h
+++ b/pandas/_libs/include/pandas/vendored/ujson/lib/ultrajson.h
@@ -53,7 +53,7 @@ tree doesn't have cyclic references.
 
 #include <stdio.h>
 #include <wchar.h>
-#include "../../headers/portable.h"
+#include "pandas/portable.h"
 
 // Don't output any extra whitespaces when encoding
 #define JSON_NO_EXTRA_WHITESPACE
diff --git a/pandas/_libs/src/ujson/python/version.h b/pandas/_libs/include/pandas/vendored/ujson/python/version.h
similarity index 100%
rename from pandas/_libs/src/ujson/python/version.h
rename to pandas/_libs/include/pandas/vendored/ujson/python/version.h
diff --git a/pandas/_libs/khash.pxd b/pandas/_libs/khash.pxd
index a9f819e5e16db..c439e1cca772b 100644
--- a/pandas/_libs/khash.pxd
+++ b/pandas/_libs/khash.pxd
@@ -15,7 +15,7 @@ from numpy cimport (
 )
 
 
-cdef extern from "khash_python.h":
+cdef extern from "pandas/vendored/klib/khash_python.h":
     const int KHASH_TRACE_DOMAIN
 
     ctypedef uint32_t khuint_t
diff --git a/pandas/_libs/khash_for_primitive_helper.pxi.in b/pandas/_libs/khash_for_primitive_helper.pxi.in
index d0934b3e0ee6e..d3391d4028938 100644
--- a/pandas/_libs/khash_for_primitive_helper.pxi.in
+++ b/pandas/_libs/khash_for_primitive_helper.pxi.in
@@ -24,7 +24,7 @@ primitive_types = [('int64', 'int64_t'),
 
 {{for name, c_type in primitive_types}}
 
-cdef extern from "khash_python.h":
+cdef extern from "pandas/vendored/klib/khash_python.h":
     ctypedef struct kh_{{name}}_t:
         khuint_t n_buckets, size, n_occupied, upper_bound
         uint32_t *flags
diff --git a/pandas/_libs/lib.pyx b/pandas/_libs/lib.pyx
index 80592d4f67c98..59a9d0752805b 100644
--- a/pandas/_libs/lib.pyx
+++ b/pandas/_libs/lib.pyx
@@ -93,7 +93,7 @@ cdef extern from "numpy/arrayobject.h":
 cdef extern from "numpy/ndarrayobject.h":
     bint PyArray_CheckScalar(obj) nogil
 
-cdef extern from "pd_parser.h":
+cdef extern from "pandas/parser/pd_parser.h":
     int floatify(object, float64_t *result, int *maybe_int) except -1
     void PandasParser_IMPORT()
 
diff --git a/pandas/_libs/meson.build b/pandas/_libs/meson.build
index 382247c63c1ad..5e59f15d0d089 100644
--- a/pandas/_libs/meson.build
+++ b/pandas/_libs/meson.build
@@ -61,44 +61,33 @@ subdir('tslibs')
 libs_sources = {
     # Dict of extension name -> dict of {sources, include_dirs, and deps}
     # numpy include dir is implicitly included
-    'algos': {'sources': ['algos.pyx', _algos_common_helper, _algos_take_helper, _khash_primitive_helper],
-              'include_dirs': klib_include},
+    'algos': {'sources': ['algos.pyx', _algos_common_helper, _algos_take_helper, _khash_primitive_helper]},
     'arrays': {'sources': ['arrays.pyx']},
     'groupby': {'sources': ['groupby.pyx']},
     'hashing': {'sources': ['hashing.pyx']},
-    'hashtable': {'sources': ['hashtable.pyx', _khash_primitive_helper, _hashtable_class_helper, _hashtable_func_helper],
-                  'include_dirs': klib_include},
-    'index': {'sources': ['index.pyx', _index_class_helper],
-              'include_dirs': [klib_include, 'tslibs']},
+    'hashtable': {'sources': ['hashtable.pyx', _khash_primitive_helper, _hashtable_class_helper, _hashtable_func_helper]},
+    'index': {'sources': ['index.pyx', _index_class_helper]},
     'indexing': {'sources': ['indexing.pyx']},
     'internals': {'sources': ['internals.pyx']},
-    'interval': {'sources': ['interval.pyx', _intervaltree_helper],
-                'include_dirs': [klib_include, 'tslibs']},
+    'interval': {'sources': ['interval.pyx', _intervaltree_helper]},
     'join': {'sources': ['join.pyx', _khash_primitive_helper],
-             'include_dirs': klib_include,
              'deps': _khash_primitive_helper_dep},
-    'lib': {'sources': ['lib.pyx', 'src/parser/tokenizer.c'],
-            'include_dirs': [klib_include, inc_datetime]},
-    'missing': {'sources': ['missing.pyx'],
-                'include_dirs': [inc_datetime]},
-    'pandas_datetime': {'sources': ['tslibs/src/datetime/np_datetime.c',
-                                    'tslibs/src/datetime/np_datetime_strings.c',
-                                    'tslibs/src/datetime/date_conversions.c',
-                                    'tslibs/src/datetime/pd_datetime.c']},
-                        #'include_dirs':
+    'lib': {'sources': ['lib.pyx', 'src/parser/tokenizer.c']},
+    'missing': {'sources': ['missing.pyx']},
+    'pandas_datetime': {'sources': ['src/vendored/numpy/datetime/np_datetime.c',
+                                    'src/vendored/numpy/datetime/np_datetime_strings.c',
+                                    'src/datetime/date_conversions.c',
+                                    'src/datetime/pd_datetime.c']},
     'pandas_parser': {'sources': ['src/parser/tokenizer.c',
                                   'src/parser/io.c',
-                                  'pd_parser.c'],
-                      'include_dirs': [klib_include]},
+                                  'src/parser/pd_parser.c']},
     'parsers': {'sources': ['parsers.pyx', 'src/parser/tokenizer.c', 'src/parser/io.c'],
-                'include_dirs': [klib_include, 'src'],
                 'deps': _khash_primitive_helper_dep},
-    'json': {'sources': ['src/ujson/python/ujson.c',
-                         'src/ujson/python/objToJSON.c',
-                         'src/ujson/python/JSONtoObj.c',
-                         'src/ujson/lib/ultrajsonenc.c',
-                         'src/ujson/lib/ultrajsondec.c'],
-             'include_dirs': ['tslibs/src/datetime', 'src/ujson/lib', 'src/ujson/python']},
+    'json': {'sources': ['src/vendored/ujson/python/ujson.c',
+                         'src/vendored/ujson/python/objToJSON.c',
+                         'src/vendored/ujson/python/JSONtoObj.c',
+                         'src/vendored/ujson/lib/ultrajsonenc.c',
+                         'src/vendored/ujson/lib/ultrajsondec.c']},
     'ops': {'sources': ['ops.pyx']},
     'ops_dispatch': {'sources': ['ops_dispatch.pyx']},
     'properties': {'sources': ['properties.pyx']},
@@ -106,8 +95,7 @@ libs_sources = {
     'sas': {'sources': ['sas.pyx']},
     'byteswap': {'sources': ['byteswap.pyx']},
     'sparse': {'sources': ['sparse.pyx', _sparse_op_helper]},
-    'tslib': {'sources': ['tslib.pyx'],
-              'include_dirs': inc_datetime},
+    'tslib': {'sources': ['tslib.pyx']},
     'testing': {'sources': ['testing.pyx']},
     'writers': {'sources': ['writers.pyx']}
 }
@@ -118,7 +106,7 @@ foreach ext_name, ext_dict : libs_sources
         ext_name,
         ext_dict.get('sources'),
         cython_args: ['--include-dir', meson.current_build_dir()],
-        include_directories: [inc_np] + ext_dict.get('include_dirs', ''),
+        include_directories: [inc_np, inc_pd],
         dependencies: ext_dict.get('deps', ''),
         subdir: 'pandas/_libs',
         install: true
diff --git a/pandas/_libs/parsers.pyx b/pandas/_libs/parsers.pyx
index a45299c8ba896..10b2427835ed1 100644
--- a/pandas/_libs/parsers.pyx
+++ b/pandas/_libs/parsers.pyx
@@ -117,7 +117,7 @@ cdef:
     int64_t DEFAULT_CHUNKSIZE = 256 * 1024
 
 
-cdef extern from "headers/portable.h":
+cdef extern from "pandas/portable.h":
     # I *think* this is here so that strcasecmp is defined on Windows
     # so we don't get
     # `parsers.obj : error LNK2001: unresolved external symbol strcasecmp`
@@ -127,7 +127,7 @@ cdef extern from "headers/portable.h":
     pass
 
 
-cdef extern from "parser/tokenizer.h":
+cdef extern from "pandas/parser/tokenizer.h":
 
     ctypedef enum ParserState:
         START_RECORD
@@ -245,7 +245,7 @@ cdef extern from "parser/tokenizer.h":
 
     void COLITER_NEXT(coliter_t, const char *) nogil
 
-cdef extern from "pd_parser.h":
+cdef extern from "pandas/parser/pd_parser.h":
     void *new_rd_source(object obj) except NULL
 
     int del_rd_source(void *src)
diff --git a/pandas/_libs/tslibs/src/datetime/date_conversions.c b/pandas/_libs/src/datetime/date_conversions.c
similarity index 94%
rename from pandas/_libs/tslibs/src/datetime/date_conversions.c
rename to pandas/_libs/src/datetime/date_conversions.c
index 190713d62d306..84fc5507010ed 100644
--- a/pandas/_libs/tslibs/src/datetime/date_conversions.c
+++ b/pandas/_libs/src/datetime/date_conversions.c
@@ -8,9 +8,9 @@ The full license is in the LICENSE file, distributed with this software.
 // Conversion routines that are useful for serialization,
 // but which don't interact with JSON objects directly
 
-#include "date_conversions.h"
-#include "np_datetime.h"
-#include "np_datetime_strings.h"
+#include "pandas/datetime/date_conversions.h"
+#include "pandas/vendored/numpy/datetime/np_datetime.h"
+#include "pandas/vendored/numpy/datetime/np_datetime_strings.h"
 
 /*
  * Function: scaleNanosecToUnit
diff --git a/pandas/_libs/tslibs/src/datetime/pd_datetime.c b/pandas/_libs/src/datetime/pd_datetime.c
similarity index 99%
rename from pandas/_libs/tslibs/src/datetime/pd_datetime.c
rename to pandas/_libs/src/datetime/pd_datetime.c
index 98b6073d7a488..fc2cbcab90174 100644
--- a/pandas/_libs/tslibs/src/datetime/pd_datetime.c
+++ b/pandas/_libs/src/datetime/pd_datetime.c
@@ -20,7 +20,7 @@ This file is derived from NumPy 1.7. See NUMPY_LICENSE.txt
 #include <Python.h>
 
 #include "datetime.h"
-#include "pd_datetime.h"
+#include "pandas/datetime/pd_datetime.h"
 
 
 static void pandas_datetime_destructor(PyObject *op) {
diff --git a/pandas/_libs/src/parser/io.c b/pandas/_libs/src/parser/io.c
index 38304cca94a12..e00c5c1e807a7 100644
--- a/pandas/_libs/src/parser/io.c
+++ b/pandas/_libs/src/parser/io.c
@@ -7,7 +7,7 @@ Distributed under the terms of the BSD Simplified License.
 The full license is in the LICENSE file, distributed with this software.
 */
 
-#include "io.h"
+#include "pandas/parser/io.h"
 
 /*
   On-disk FILE, uncompressed
diff --git a/pandas/_libs/pd_parser.c b/pandas/_libs/src/parser/pd_parser.c
similarity index 98%
rename from pandas/_libs/pd_parser.c
rename to pandas/_libs/src/parser/pd_parser.c
index 15d82b59df3e8..c429f17c1cb8b 100644
--- a/pandas/_libs/pd_parser.c
+++ b/pandas/_libs/src/parser/pd_parser.c
@@ -8,8 +8,8 @@ Distributed under the terms of the BSD Simplified License.
 */
 #define _PANDAS_PARSER_IMPL
 
-#include "pd_parser.h"
-#include "src/parser/io.h"
+#include "pandas/parser/pd_parser.h"
+#include "pandas/parser/io.h"
 
 static int to_double(char *item, double *p_value, char sci, char decimal,
                             int *maybe_int) {
diff --git a/pandas/_libs/src/parser/tokenizer.c b/pandas/_libs/src/parser/tokenizer.c
index e60fc6bf75f91..abd3fb9e1fef3 100644
--- a/pandas/_libs/src/parser/tokenizer.c
+++ b/pandas/_libs/src/parser/tokenizer.c
@@ -17,13 +17,13 @@ GitHub. See Python Software Foundation License and BSD licenses for these.
 
 */
 
-#include "tokenizer.h"
+#include "pandas/parser/tokenizer.h"
 
 #include <ctype.h>
 #include <float.h>
 #include <math.h>
 
-#include "../headers/portable.h"
+#include "pandas/portable.h"
 
 void coliter_setup(coliter_t *self, parser_t *parser, int64_t i,
                    int64_t start) {
diff --git a/pandas/_libs/tslibs/src/datetime/np_datetime.c b/pandas/_libs/src/vendored/numpy/datetime/np_datetime.c
similarity index 99%
rename from pandas/_libs/tslibs/src/datetime/np_datetime.c
rename to pandas/_libs/src/vendored/numpy/datetime/np_datetime.c
index e4d9c5dcd63ea..7e5cb53cf8f62 100644
--- a/pandas/_libs/tslibs/src/datetime/np_datetime.c
+++ b/pandas/_libs/src/vendored/numpy/datetime/np_datetime.c
@@ -25,7 +25,7 @@ This file is derived from NumPy 1.7. See NUMPY_LICENSE.txt
 #include <numpy/arrayobject.h>
 #include <numpy/arrayscalars.h>
 #include <numpy/ndarraytypes.h>
-#include "np_datetime.h"
+#include "pandas/vendored/numpy/datetime/np_datetime.h"
 
 
 const int days_per_month_table[2][12] = {
diff --git a/pandas/_libs/tslibs/src/datetime/np_datetime_strings.c b/pandas/_libs/src/vendored/numpy/datetime/np_datetime_strings.c
similarity index 99%
rename from pandas/_libs/tslibs/src/datetime/np_datetime_strings.c
rename to pandas/_libs/src/vendored/numpy/datetime/np_datetime_strings.c
index f1f03e6467eac..629d88ca6f589 100644
--- a/pandas/_libs/tslibs/src/datetime/np_datetime_strings.c
+++ b/pandas/_libs/src/vendored/numpy/datetime/np_datetime_strings.c
@@ -34,8 +34,8 @@ This file implements string parsing and creation for NumPy datetime.
 #include <numpy/arrayscalars.h>
 #include <numpy/ndarraytypes.h>
 
-#include "np_datetime.h"
-#include "np_datetime_strings.h"
+#include "pandas/vendored/numpy/datetime/np_datetime.h"
+#include "pandas/vendored/numpy/datetime/np_datetime_strings.h"
 
 
 /*
diff --git a/pandas/_libs/src/ujson/lib/ultrajsondec.c b/pandas/_libs/src/vendored/ujson/lib/ultrajsondec.c
similarity index 99%
rename from pandas/_libs/src/ujson/lib/ultrajsondec.c
rename to pandas/_libs/src/vendored/ujson/lib/ultrajsondec.c
index 5347db1655669..9ec12cb242728 100644
--- a/pandas/_libs/src/ujson/lib/ultrajsondec.c
+++ b/pandas/_libs/src/vendored/ujson/lib/ultrajsondec.c
@@ -46,7 +46,7 @@ Numeric decoder derived from TCL library
 #include <stdlib.h>
 #include <string.h>
 #include <wchar.h>
-#include "ultrajson.h"
+#include "pandas/vendored/ujson/lib/ultrajson.h"
 
 #ifndef TRUE
 #define TRUE 1
diff --git a/pandas/_libs/src/ujson/lib/ultrajsonenc.c b/pandas/_libs/src/vendored/ujson/lib/ultrajsonenc.c
similarity index 99%
rename from pandas/_libs/src/ujson/lib/ultrajsonenc.c
rename to pandas/_libs/src/vendored/ujson/lib/ultrajsonenc.c
index 169c5b6889077..726676799af65 100644
--- a/pandas/_libs/src/ujson/lib/ultrajsonenc.c
+++ b/pandas/_libs/src/vendored/ujson/lib/ultrajsonenc.c
@@ -45,7 +45,7 @@ Numeric decoder derived from TCL library
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include "ultrajson.h"
+#include "pandas/vendored/ujson/lib/ultrajson.h"
 
 #ifndef TRUE
 #define TRUE 1
diff --git a/pandas/_libs/src/ujson/python/JSONtoObj.c b/pandas/_libs/src/vendored/ujson/python/JSONtoObj.c
similarity index 99%
rename from pandas/_libs/src/ujson/python/JSONtoObj.c
rename to pandas/_libs/src/vendored/ujson/python/JSONtoObj.c
index d7086ffba623a..f4055fcedcfa6 100644
--- a/pandas/_libs/src/ujson/python/JSONtoObj.c
+++ b/pandas/_libs/src/vendored/ujson/python/JSONtoObj.c
@@ -40,7 +40,7 @@ Numeric decoder derived from TCL library
 #define PY_SSIZE_T_CLEAN
 #include <Python.h>
 #include <numpy/arrayobject.h>
-#include <ultrajson.h>
+#include "pandas/vendored/ujson/lib/ultrajson.h"
 
 #define PRINTMARK()
 
diff --git a/pandas/_libs/src/ujson/python/objToJSON.c b/pandas/_libs/src/vendored/ujson/python/objToJSON.c
similarity index 99%
rename from pandas/_libs/src/ujson/python/objToJSON.c
rename to pandas/_libs/src/vendored/ujson/python/objToJSON.c
index 1b8ba8f3f7e6c..65b468f268d75 100644
--- a/pandas/_libs/src/ujson/python/objToJSON.c
+++ b/pandas/_libs/src/vendored/ujson/python/objToJSON.c
@@ -46,9 +46,9 @@ Numeric decoder derived from TCL library
 #include <numpy/arrayscalars.h>
 #include <numpy/ndarraytypes.h>
 #include <numpy/npy_math.h>
-#include <ultrajson.h>
+#include "pandas/vendored/ujson/lib/ultrajson.h"
 #include "datetime.h"
-#include "pd_datetime.h"
+#include "pandas/datetime/pd_datetime.h"
 
 npy_int64 get_nat(void) { return NPY_MIN_INT64; }
 
diff --git a/pandas/_libs/src/ujson/python/ujson.c b/pandas/_libs/src/vendored/ujson/python/ujson.c
similarity index 99%
rename from pandas/_libs/src/ujson/python/ujson.c
rename to pandas/_libs/src/vendored/ujson/python/ujson.c
index 5c87ee6dd7ddc..15ea4b056b02d 100644
--- a/pandas/_libs/src/ujson/python/ujson.c
+++ b/pandas/_libs/src/vendored/ujson/python/ujson.c
@@ -35,7 +35,7 @@ Numeric decoder derived from TCL library
 * Copyright (c) 1994 Sun Microsystems, Inc.
 */
 
-#include "version.h"
+#include "pandas/vendored/ujson/python/version.h"
 #define PY_SSIZE_T_CLEAN
 #include <Python.h>
 #define PY_ARRAY_UNIQUE_SYMBOL UJSON_NUMPY
diff --git a/pandas/_libs/tslibs/meson.build b/pandas/_libs/tslibs/meson.build
index fc8c9e609c416..4a51f8dc1e461 100644
--- a/pandas/_libs/tslibs/meson.build
+++ b/pandas/_libs/tslibs/meson.build
@@ -4,30 +4,19 @@ tslibs_sources = {
     'base': {'sources': ['base.pyx']},
     'ccalendar': {'sources': ['ccalendar.pyx']},
     'dtypes': {'sources': ['dtypes.pyx']},
-    'conversion': {'sources': ['conversion.pyx', 'src/datetime/np_datetime.c'],
-                   'include_dirs': inc_datetime},
-    'fields': {'sources': ['fields.pyx', 'src/datetime/np_datetime.c']},
+    'conversion': {'sources': ['conversion.pyx']},
+    'fields': {'sources': ['fields.pyx']},
     'nattype': {'sources': ['nattype.pyx']},
-    'np_datetime': {'sources': ['np_datetime.pyx', 'src/datetime/np_datetime.c', 'src/datetime/np_datetime_strings.c'],
-                    'include_dirs': inc_datetime},
-    'offsets': {'sources': ['offsets.pyx', 'src/datetime/np_datetime.c'],
-                'include_dirs': inc_datetime},
-    'parsing': {'sources': ['parsing.pyx', '../src/parser/tokenizer.c'],
-                'include_dirs': klib_include},
-    'period': {'sources': ['period.pyx', 'src/datetime/np_datetime.c'],
-                'include_dirs': inc_datetime},
-    'strptime': {'sources': ['strptime.pyx', 'src/datetime/np_datetime.c'],
-                'include_dirs': inc_datetime},
-    'timedeltas': {'sources': ['timedeltas.pyx', 'src/datetime/np_datetime.c'],
-                   'include_dirs': inc_datetime},
-    'timestamps': {'sources': ['timestamps.pyx', 'src/datetime/np_datetime.c'],
-                   'include_dirs': inc_datetime},
-    'timezones': {'sources': ['timezones.pyx', 'src/datetime/np_datetime.c'],
-                  'include_dirs': inc_datetime},
-    'tzconversion': {'sources': ['tzconversion.pyx', 'src/datetime/np_datetime.c'],
-                     'include_dirs': inc_datetime},
-    'vectorized': {'sources': ['vectorized.pyx', 'src/datetime/np_datetime.c'],
-                    'include_dirs': inc_datetime}
+    'np_datetime': {'sources': ['np_datetime.pyx']},
+    'offsets': {'sources': ['offsets.pyx']},
+    'parsing': {'sources': ['parsing.pyx', '../src/parser/tokenizer.c']},
+    'period': {'sources': ['period.pyx']},
+    'strptime': {'sources': ['strptime.pyx']},
+    'timedeltas': {'sources': ['timedeltas.pyx']},
+    'timestamps': {'sources': ['timestamps.pyx']},
+    'timezones': {'sources': ['timezones.pyx']},
+    'tzconversion': {'sources': ['tzconversion.pyx']},
+    'vectorized': {'sources': ['vectorized.pyx']},
 }
 
 foreach ext_name, ext_dict : tslibs_sources
@@ -35,7 +24,7 @@ foreach ext_name, ext_dict : tslibs_sources
         ext_name,
         ext_dict.get('sources'),
         cython_args: ['--include-dir', meson.current_build_dir()],
-        include_directories: [inc_np] + ext_dict.get('include_dirs', ''),
+        include_directories: [inc_np, inc_pd],
         dependencies: ext_dict.get('deps', ''),
         subdir: 'pandas/_libs/tslibs',
         install: true
diff --git a/pandas/_libs/tslibs/np_datetime.pxd b/pandas/_libs/tslibs/np_datetime.pxd
index 15230c47ae252..60532174e8bdc 100644
--- a/pandas/_libs/tslibs/np_datetime.pxd
+++ b/pandas/_libs/tslibs/np_datetime.pxd
@@ -55,7 +55,7 @@ cdef extern from "numpy/ndarraytypes.h":
     int64_t NPY_DATETIME_NAT  # elswhere we call this NPY_NAT
 
 
-cdef extern from "src/datetime/pd_datetime.h":
+cdef extern from "pandas/datetime/pd_datetime.h":
     ctypedef struct pandas_timedeltastruct:
         int64_t days
         int32_t hrs, min, sec, ms, us, ns, seconds, microseconds, nanoseconds
diff --git a/pandas/_libs/tslibs/np_datetime.pyx b/pandas/_libs/tslibs/np_datetime.pyx
index 2eebde982789c..990f862c3d105 100644
--- a/pandas/_libs/tslibs/np_datetime.pyx
+++ b/pandas/_libs/tslibs/np_datetime.pyx
@@ -36,7 +36,7 @@ from numpy cimport (
 from pandas._libs.tslibs.util cimport get_c_string_buf_and_size
 
 
-cdef extern from "src/datetime/pd_datetime.h":
+cdef extern from "pandas/datetime/pd_datetime.h":
     int cmp_npy_datetimestruct(npy_datetimestruct *a,
                                npy_datetimestruct *b)
 
diff --git a/pandas/_libs/tslibs/parsing.pyx b/pandas/_libs/tslibs/parsing.pyx
index 71550824525eb..536ae7ee4673b 100644
--- a/pandas/_libs/tslibs/parsing.pyx
+++ b/pandas/_libs/tslibs/parsing.pyx
@@ -83,10 +83,10 @@ from pandas._libs.tslibs.util cimport (
 )
 
 
-cdef extern from "../src/headers/portable.h":
+cdef extern from "pandas/portable.h":
     int getdigit_ascii(char c, int default) nogil
 
-cdef extern from "../src/parser/tokenizer.h":
+cdef extern from "pandas/parser/tokenizer.h":
     double xstrtod(const char *p, char **q, char decimal, char sci, char tsep,
                    int skip_trailing, int *error, int *maybe_int)
 
diff --git a/pandas/_libs/window/aggregations.pyx b/pandas/_libs/window/aggregations.pyx
index c444e3b2bb71e..b0dac23c3b8e2 100644
--- a/pandas/_libs/window/aggregations.pyx
+++ b/pandas/_libs/window/aggregations.pyx
@@ -26,7 +26,7 @@ import cython
 from pandas._libs.algos import is_monotonic
 
 
-cdef extern from "../src/skiplist.h":
+cdef extern from "pandas/skiplist.h":
     ctypedef struct node_t:
         node_t **next
         int *width
diff --git a/pandas/_libs/window/meson.build b/pandas/_libs/window/meson.build
index 7d7c34a57c6a6..61719a35b2346 100644
--- a/pandas/_libs/window/meson.build
+++ b/pandas/_libs/window/meson.build
@@ -1,7 +1,7 @@
 py.extension_module(
     'aggregations',
     ['aggregations.pyx'],
-    include_directories: [inc_np, '../src'],
+    include_directories: [inc_np, inc_pd],
     dependencies: [py_dep],
     subdir: 'pandas/_libs/window',
     override_options : ['cython_language=cpp'],
@@ -11,7 +11,7 @@ py.extension_module(
 py.extension_module(
     'indexers',
     ['indexers.pyx'],
-    include_directories: [inc_np],
+    include_directories: [inc_np, inc_pd],
     dependencies: [py_dep],
     subdir: 'pandas/_libs/window',
     install: true
diff --git a/pandas/meson.build b/pandas/meson.build
index 491a08e6c0261..ab84fd688b762 100644
--- a/pandas/meson.build
+++ b/pandas/meson.build
@@ -7,8 +7,7 @@ incdir_numpy = run_command(py,
 ).stdout().strip()
 
 inc_np = include_directories(incdir_numpy)
-klib_include = include_directories('_libs/src/klib')
-inc_datetime = include_directories('_libs/tslibs')
+inc_pd = include_directories('_libs/include')
 
 fs.copyfile('__init__.py')
 
diff --git a/setup.py b/setup.py
index ee444f1aaeb85..e285299cfc05e 100755
--- a/setup.py
+++ b/setup.py
@@ -115,15 +115,14 @@ def initialize_options(self):
         self._clean_trees = []
 
         base = pjoin("pandas", "_libs", "src")
-        tsbase = pjoin("pandas", "_libs", "tslibs", "src")
-        dt = pjoin(tsbase, "datetime")
-        util = pjoin("pandas", "util")
         parser = pjoin(base, "parser")
-        ujson_python = pjoin(base, "ujson", "python")
-        ujson_lib = pjoin(base, "ujson", "lib")
+        vendored = pjoin(base, "vendored")
+        dt = pjoin(base, "datetime")
+        ujson_python = pjoin(vendored, "ujson", "python")
+        ujson_lib = pjoin(vendored, "ujson", "lib")
         self._clean_exclude = [
-            pjoin(dt, "np_datetime.c"),
-            pjoin(dt, "np_datetime_strings.c"),
+            pjoin(vendored, "numpy", "datetime", "np_datetime.c"),
+            pjoin(vendored, "numpy", "datetime", "np_datetime_strings.c"),
             pjoin(dt, "date_conversions.c"),
             pjoin(parser, "tokenizer.c"),
             pjoin(parser, "io.c"),
@@ -132,9 +131,8 @@ def initialize_options(self):
             pjoin(ujson_python, "JSONtoObj.c"),
             pjoin(ujson_lib, "ultrajsonenc.c"),
             pjoin(ujson_lib, "ultrajsondec.c"),
-            pjoin(util, "move.c"),
-            pjoin(tsbase, "datetime", "pd_datetime.c"),
-            pjoin("pandas", "_libs", "pd_parser.c"),
+            pjoin(dt, "pd_datetime.c"),
+            pjoin(parser, "pd_parser.c"),
         ]
 
         for root, dirs, files in os.walk("pandas"):
@@ -431,19 +429,15 @@ def srcpath(name=None, suffix=".pyx", subdir="src"):
     return pjoin("pandas", subdir, name + suffix)
 
 
-lib_depends = ["pandas/_libs/src/parse_helper.h"]
+lib_depends = ["pandas/_libs/include/pandas/parse_helper.h"]
 
-klib_include = ["pandas/_libs/src/klib"]
-
-tseries_includes = ["pandas/_libs/tslibs/src/datetime"]
 tseries_depends = [
-    "pandas/_libs/tslibs/src/datetime/pd_datetime.h",
+    "pandas/_libs/include/pandas/datetime/pd_datetime.h",
 ]
 
 ext_data = {
     "_libs.algos": {
         "pyxfile": "_libs/algos",
-        "include": klib_include,
         "depends": _pxi_dep["algos"],
     },
     "_libs.arrays": {"pyxfile": "_libs/arrays"},
@@ -451,34 +445,32 @@ def srcpath(name=None, suffix=".pyx", subdir="src"):
     "_libs.hashing": {"pyxfile": "_libs/hashing", "depends": []},
     "_libs.hashtable": {
         "pyxfile": "_libs/hashtable",
-        "include": klib_include,
         "depends": (
-            ["pandas/_libs/src/klib/khash_python.h", "pandas/_libs/src/klib/khash.h"]
+            [
+                "pandas/_libs/include/pandas/vendored/klib/khash_python.h",
+                "pandas/_libs/include/pandas/vendored/klib/khash.h",
+            ]
             + _pxi_dep["hashtable"]
         ),
     },
     "_libs.index": {
         "pyxfile": "_libs/index",
-        "include": klib_include,
         "depends": _pxi_dep["index"],
     },
     "_libs.indexing": {"pyxfile": "_libs/indexing"},
     "_libs.internals": {"pyxfile": "_libs/internals"},
     "_libs.interval": {
         "pyxfile": "_libs/interval",
-        "include": klib_include,
         "depends": _pxi_dep["interval"],
     },
-    "_libs.join": {"pyxfile": "_libs/join", "include": klib_include},
+    "_libs.join": {"pyxfile": "_libs/join"},
     "_libs.lib": {
         "pyxfile": "_libs/lib",
         "depends": lib_depends + tseries_depends,
-        "include": klib_include,  # due to tokenizer import
     },
     "_libs.missing": {"pyxfile": "_libs/missing", "depends": tseries_depends},
     "_libs.parsers": {
         "pyxfile": "_libs/parsers",
-        "include": klib_include + ["pandas/_libs/src", "pandas/_libs"],
         "depends": [
             "pandas/_libs/src/parser/tokenizer.h",
             "pandas/_libs/src/parser/io.h",
@@ -500,7 +492,6 @@ def srcpath(name=None, suffix=".pyx", subdir="src"):
     "_libs.tslibs.conversion": {
         "pyxfile": "_libs/tslibs/conversion",
         "depends": tseries_depends,
-        "include": klib_include,
     },
     "_libs.tslibs.fields": {
         "pyxfile": "_libs/tslibs/fields",
@@ -510,17 +501,13 @@ def srcpath(name=None, suffix=".pyx", subdir="src"):
     "_libs.tslibs.np_datetime": {
         "pyxfile": "_libs/tslibs/np_datetime",
         "depends": tseries_depends,
-        "includes": tseries_includes,
     },
     "_libs.tslibs.offsets": {
         "pyxfile": "_libs/tslibs/offsets",
         "depends": tseries_depends,
-        "includes": tseries_includes,
     },
     "_libs.tslibs.parsing": {
         "pyxfile": "_libs/tslibs/parsing",
-        "include": tseries_includes + klib_include,
-        "depends": ["pandas/_libs/src/parser/tokenizer.h"],
         "sources": ["pandas/_libs/src/parser/tokenizer.c"],
     },
     "_libs.tslibs.period": {
@@ -537,7 +524,6 @@ def srcpath(name=None, suffix=".pyx", subdir="src"):
     },
     "_libs.tslibs.timestamps": {
         "pyxfile": "_libs/tslibs/timestamps",
-        "include": tseries_includes,
         "depends": tseries_depends,
     },
     "_libs.tslibs.timezones": {"pyxfile": "_libs/tslibs/timezones"},
@@ -554,7 +540,7 @@ def srcpath(name=None, suffix=".pyx", subdir="src"):
         "pyxfile": "_libs/window/aggregations",
         "language": "c++",
         "suffix": ".cpp",
-        "depends": ["pandas/_libs/src/skiplist.h"],
+        "depends": ["pandas/_libs/include/pandas/skiplist.h"],
     },
     "_libs.window.indexers": {"pyxfile": "_libs/window/indexers"},
     "_libs.writers": {"pyxfile": "_libs/writers"},
@@ -571,8 +557,7 @@ def srcpath(name=None, suffix=".pyx", subdir="src"):
 
     sources.extend(data.get("sources", []))
 
-    include = data.get("include", [])
-    include.append(numpy.get_include())
+    include = ["pandas/_libs/include", numpy.get_include()]
 
     undef_macros = []
 
@@ -612,24 +597,22 @@ def srcpath(name=None, suffix=".pyx", subdir="src"):
 ujson_ext = Extension(
     "pandas._libs.json",
     depends=[
-        "pandas/_libs/src/ujson/lib/ultrajson.h",
-        "pandas/_libs/tslibs/src/datetime/pd_datetime.h",
+        "pandas/_libs/include/pandas/vendored/ujson/lib/ultrajson.h",
+        "pandas/_libs/include/pandas/datetime/pd_datetime.h",
     ],
     sources=(
         [
-            "pandas/_libs/src/ujson/python/ujson.c",
-            "pandas/_libs/src/ujson/python/objToJSON.c",
-            "pandas/_libs/src/ujson/python/JSONtoObj.c",
-            "pandas/_libs/src/ujson/lib/ultrajsonenc.c",
-            "pandas/_libs/src/ujson/lib/ultrajsondec.c",
+            "pandas/_libs/src/vendored/ujson/python/ujson.c",
+            "pandas/_libs/src/vendored/ujson/python/objToJSON.c",
+            "pandas/_libs/src/vendored/ujson/python/JSONtoObj.c",
+            "pandas/_libs/src/vendored/ujson/lib/ultrajsonenc.c",
+            "pandas/_libs/src/vendored/ujson/lib/ultrajsondec.c",
         ]
     ),
     include_dirs=[
-        "pandas/_libs/src/ujson/python",
-        "pandas/_libs/src/ujson/lib",
+        "pandas/_libs/include",
         numpy.get_include(),
-    ]
-    + tseries_includes,
+    ],
     extra_compile_args=(extra_compile_args),
     extra_link_args=extra_link_args,
     define_macros=macros,
@@ -647,14 +630,14 @@ def srcpath(name=None, suffix=".pyx", subdir="src"):
     depends=["pandas/_libs/tslibs/datetime/pd_datetime.h"],
     sources=(
         [
-            "pandas/_libs/tslibs/src/datetime/np_datetime.c",
-            "pandas/_libs/tslibs/src/datetime/np_datetime_strings.c",
-            "pandas/_libs/tslibs/src/datetime/date_conversions.c",
-            "pandas/_libs/tslibs/src/datetime/pd_datetime.c",
+            "pandas/_libs/src/vendored/numpy/datetime/np_datetime.c",
+            "pandas/_libs/src/vendored/numpy/datetime/np_datetime_strings.c",
+            "pandas/_libs/src/datetime/date_conversions.c",
+            "pandas/_libs/src/datetime/pd_datetime.c",
         ]
     ),
-    include_dirs=tseries_includes
-    + [
+    include_dirs=[
+        "pandas/_libs/include",
         numpy.get_include(),
     ],
     extra_compile_args=(extra_compile_args),
@@ -671,16 +654,16 @@ def srcpath(name=None, suffix=".pyx", subdir="src"):
 # pd_datetime
 pd_parser_ext = Extension(
     "pandas._libs.pandas_parser",
-    depends=["pandas/_libs/pd_parser.h"],
+    depends=["pandas/_libs/include/pandas/parser/pd_parser.h"],
     sources=(
         [
             "pandas/_libs/src/parser/tokenizer.c",
             "pandas/_libs/src/parser/io.c",
-            "pandas/_libs/pd_parser.c",
+            "pandas/_libs/src/parser/pd_parser.c",
         ]
     ),
     include_dirs=[
-        "pandas/_libs/src/klib",
+        "pandas/_libs/include",
     ],
     extra_compile_args=(extra_compile_args),
     extra_link_args=extra_link_args,