diff --git a/doc/source/whatsnew/v1.3.0.rst b/doc/source/whatsnew/v1.3.0.rst
index 1d76c9d296255..d90ccd57be16a 100644
--- a/doc/source/whatsnew/v1.3.0.rst
+++ b/doc/source/whatsnew/v1.3.0.rst
@@ -192,6 +192,7 @@ Categorical
 - Bug in ``CategoricalIndex.reindex`` failed when ``Index`` passed with elements all in category (:issue:`28690`)
 - Bug where constructing a :class:`Categorical` from an object-dtype array of ``date`` objects did not round-trip correctly with ``astype`` (:issue:`38552`)
 - Bug in constructing a :class:`DataFrame` from an ``ndarray`` and a :class:`CategoricalDtype` (:issue:`38857`)
+- Bug in :meth:`DataFrame.reindex` was throwing ``IndexError`` when new index contained duplicates and old index was :class:`CategoricalIndex` (:issue:`38906`)
 
 Datetimelike
 ^^^^^^^^^^^^
diff --git a/pandas/core/indexes/base.py b/pandas/core/indexes/base.py
index 92a4d0a125195..a2e9737f305ba 100644
--- a/pandas/core/indexes/base.py
+++ b/pandas/core/indexes/base.py
@@ -3730,8 +3730,13 @@ def _reindex_non_unique(self, target):
             new_labels[cur_indexer] = cur_labels
             new_labels[missing_indexer] = missing_labels
 
+            # GH#38906
+            if not len(self):
+
+                new_indexer = np.arange(0)
+
             # a unique indexer
-            if target.is_unique:
+            elif target.is_unique:
 
                 # see GH5553, make sure we use the right indexer
                 new_indexer = np.arange(len(indexer))
diff --git a/pandas/tests/frame/indexing/test_indexing.py b/pandas/tests/frame/indexing/test_indexing.py
index 4cbdf61ff8dae..2b80e06861a00 100644
--- a/pandas/tests/frame/indexing/test_indexing.py
+++ b/pandas/tests/frame/indexing/test_indexing.py
@@ -1717,6 +1717,34 @@ def test_setitem(self, uint64_frame):
         )
 
 
+@pytest.mark.parametrize(
+    "src_idx",
+    [
+        Index([]),
+        pd.CategoricalIndex([]),
+    ],
+)
+@pytest.mark.parametrize(
+    "cat_idx",
+    [
+        # No duplicates
+        Index([]),
+        pd.CategoricalIndex([]),
+        Index(["A", "B"]),
+        pd.CategoricalIndex(["A", "B"]),
+        # Duplicates: GH#38906
+        Index(["A", "A"]),
+        pd.CategoricalIndex(["A", "A"]),
+    ],
+)
+def test_reindex_empty(src_idx, cat_idx):
+    df = DataFrame(columns=src_idx, index=["K"], dtype="f8")
+
+    result = df.reindex(columns=cat_idx)
+    expected = DataFrame(index=["K"], columns=cat_idx, dtype="f8")
+    tm.assert_frame_equal(result, expected)
+
+
 def test_object_casting_indexing_wraps_datetimelike():
     # GH#31649, check the indexing methods all the way down the stack
     df = DataFrame(