diff --git a/asv_bench/benchmarks/arithmetic.py b/asv_bench/benchmarks/arithmetic.py
index 496db66c78569..4f84e0a562687 100644
--- a/asv_bench/benchmarks/arithmetic.py
+++ b/asv_bench/benchmarks/arithmetic.py
@@ -106,6 +106,10 @@ def time_frame_op_with_series_axis0(self, opname):
     def time_frame_op_with_series_axis1(self, opname):
         getattr(operator, opname)(self.df, self.ser)
 
+    # exclude comparisons from the params for time_frame_op_with_series_axis1
+    #  since they do not do alignment so raise
+    time_frame_op_with_series_axis1.params = [params[0][6:]]
+
 
 class FrameWithFrameWide:
     # Many-columns, mixed dtypes
diff --git a/doc/source/whatsnew/v2.0.0.rst b/doc/source/whatsnew/v2.0.0.rst
index 1fb9a81e85a83..03ea1aa5b8f9f 100644
--- a/doc/source/whatsnew/v2.0.0.rst
+++ b/doc/source/whatsnew/v2.0.0.rst
@@ -569,6 +569,7 @@ Removal of prior version deprecations/changes
 - Enforced deprecation of calling numpy "ufunc"s on :class:`DataFrame` with ``method="outer"``; this now raises ``NotImplementedError`` (:issue:`36955`)
 - Enforced deprecation disallowing passing ``numeric_only=True`` to :class:`Series` reductions (``rank``, ``any``, ``all``, ...) with non-numeric dtype (:issue:`47500`)
 - Changed behavior of :meth:`DataFrameGroupBy.apply` and :meth:`SeriesGroupBy.apply` so that ``group_keys`` is respected even if a transformer is detected (:issue:`34998`)
+- Comparisons between a :class:`DataFrame` and a :class:`Series` where the frame's columns do not match the series's index raise ``ValueError`` instead of automatically aligning, do ``left, right = left.align(right, axis=1, copy=False)`` before comparing (:issue:`36795`)
 - Enforced deprecation ``numeric_only=None`` (the default) in DataFrame reductions that would silently drop columns that raised; ``numeric_only`` now defaults to ``False`` (:issue:`41480`)
 - Changed default of ``numeric_only`` to ``False`` in all DataFrame methods with that argument (:issue:`46096`, :issue:`46906`)
 - Changed default of ``numeric_only`` to ``False`` in :meth:`Series.rank` (:issue:`47561`)
diff --git a/pandas/core/ops/__init__.py b/pandas/core/ops/__init__.py
index af27ff67599ac..bfedaca093a8e 100644
--- a/pandas/core/ops/__init__.py
+++ b/pandas/core/ops/__init__.py
@@ -7,7 +7,6 @@
 
 import operator
 from typing import TYPE_CHECKING
-import warnings
 
 import numpy as np
 
@@ -18,7 +17,6 @@
     Level,
 )
 from pandas.util._decorators import Appender
-from pandas.util._exceptions import find_stack_level
 
 from pandas.core.dtypes.common import (
     is_array_like,
@@ -299,13 +297,10 @@ def to_series(right):
 
         if not flex:
             if not left.axes[axis].equals(right.index):
-                warnings.warn(
-                    "Automatic reindexing on DataFrame vs Series comparisons "
-                    "is deprecated and will raise ValueError in a future version. "
-                    "Do `left, right = left.align(right, axis=1, copy=False)` "
-                    "before e.g. `left == right`",
-                    FutureWarning,
-                    stacklevel=find_stack_level(),
+                raise ValueError(
+                    "Operands are not aligned. Do "
+                    "`left, right = left.align(right, axis=1, copy=False)` "
+                    "before operating."
                 )
 
         left, right = left.align(
diff --git a/pandas/tests/arithmetic/test_datetime64.py b/pandas/tests/arithmetic/test_datetime64.py
index bad5335ad2d58..b4f1c5404d178 100644
--- a/pandas/tests/arithmetic/test_datetime64.py
+++ b/pandas/tests/arithmetic/test_datetime64.py
@@ -307,43 +307,60 @@ def test_timestamp_compare_series(self, left, right):
 
     def test_dt64arr_timestamp_equality(self, box_with_array):
         # GH#11034
+        box = box_with_array
 
         ser = Series([Timestamp("2000-01-29 01:59:00"), Timestamp("2000-01-30"), NaT])
-        ser = tm.box_expected(ser, box_with_array)
+        ser = tm.box_expected(ser, box)
         xbox = get_upcast_box(ser, ser, True)
 
         result = ser != ser
         expected = tm.box_expected([False, False, True], xbox)
         tm.assert_equal(result, expected)
 
-        warn = FutureWarning if box_with_array is pd.DataFrame else None
-        with tm.assert_produces_warning(warn):
+        if box is pd.DataFrame:
             # alignment for frame vs series comparisons deprecated
+            #  in GH#46795 enforced 2.0
+            with pytest.raises(ValueError, match="not aligned"):
+                ser != ser[0]
+
+        else:
             result = ser != ser[0]
-        expected = tm.box_expected([False, True, True], xbox)
-        tm.assert_equal(result, expected)
+            expected = tm.box_expected([False, True, True], xbox)
+            tm.assert_equal(result, expected)
 
-        with tm.assert_produces_warning(warn):
+        if box is pd.DataFrame:
             # alignment for frame vs series comparisons deprecated
+            #  in GH#46795 enforced 2.0
+            with pytest.raises(ValueError, match="not aligned"):
+                ser != ser[2]
+        else:
             result = ser != ser[2]
-        expected = tm.box_expected([True, True, True], xbox)
-        tm.assert_equal(result, expected)
+            expected = tm.box_expected([True, True, True], xbox)
+            tm.assert_equal(result, expected)
 
         result = ser == ser
         expected = tm.box_expected([True, True, False], xbox)
         tm.assert_equal(result, expected)
 
-        with tm.assert_produces_warning(warn):
+        if box is pd.DataFrame:
             # alignment for frame vs series comparisons deprecated
+            #  in GH#46795 enforced 2.0
+            with pytest.raises(ValueError, match="not aligned"):
+                ser == ser[0]
+        else:
             result = ser == ser[0]
-        expected = tm.box_expected([True, False, False], xbox)
-        tm.assert_equal(result, expected)
+            expected = tm.box_expected([True, False, False], xbox)
+            tm.assert_equal(result, expected)
 
-        with tm.assert_produces_warning(warn):
+        if box is pd.DataFrame:
             # alignment for frame vs series comparisons deprecated
+            #  in GH#46795 enforced 2.0
+            with pytest.raises(ValueError, match="not aligned"):
+                ser == ser[2]
+        else:
             result = ser == ser[2]
-        expected = tm.box_expected([False, False, False], xbox)
-        tm.assert_equal(result, expected)
+            expected = tm.box_expected([False, False, False], xbox)
+            tm.assert_equal(result, expected)
 
     @pytest.mark.parametrize(
         "datetimelike",
diff --git a/pandas/tests/frame/test_arithmetic.py b/pandas/tests/frame/test_arithmetic.py
index 545482e6d3dad..8aedac036c2c9 100644
--- a/pandas/tests/frame/test_arithmetic.py
+++ b/pandas/tests/frame/test_arithmetic.py
@@ -1164,19 +1164,15 @@ def test_frame_with_zero_len_series_corner_cases():
     expected = DataFrame(df.values * np.nan, columns=df.columns)
     tm.assert_frame_equal(result, expected)
 
-    with tm.assert_produces_warning(FutureWarning):
-        # Automatic alignment for comparisons deprecated
-        result = df == ser
-    expected = DataFrame(False, index=df.index, columns=df.columns)
-    tm.assert_frame_equal(result, expected)
+    with pytest.raises(ValueError, match="not aligned"):
+        # Automatic alignment for comparisons deprecated GH#36795, enforced 2.0
+        df == ser
 
-    # non-float case should not raise on comparison
+    # non-float case should not raise TypeError on comparison
     df2 = DataFrame(df.values.view("M8[ns]"), columns=df.columns)
-    with tm.assert_produces_warning(FutureWarning):
+    with pytest.raises(ValueError, match="not aligned"):
         # Automatic alignment for comparisons deprecated
-        result = df2 == ser
-    expected = DataFrame(False, index=df.index, columns=df.columns)
-    tm.assert_frame_equal(result, expected)
+        df2 == ser
 
 
 def test_zero_len_frame_with_series_corner_cases():
diff --git a/pandas/tests/generic/test_finalize.py b/pandas/tests/generic/test_finalize.py
index a7551af68bc2b..c39973d7649e8 100644
--- a/pandas/tests/generic/test_finalize.py
+++ b/pandas/tests/generic/test_finalize.py
@@ -476,9 +476,6 @@ def test_finalize_called_eval_numexpr():
 # Binary operations
 
 
-@pytest.mark.filterwarnings(
-    "ignore:Automatic reindexing on DataFrame vs Series:FutureWarning"
-)
 @pytest.mark.parametrize("annotate", ["left", "right", "both"])
 @pytest.mark.parametrize(
     "args",
@@ -504,6 +501,20 @@ def test_binops(request, args, annotate, all_binary_operators):
     if annotate in {"left", "both"} and not isinstance(right, int):
         right.attrs = {"a": 1}
 
+    is_cmp = all_binary_operators in [
+        operator.eq,
+        operator.ne,
+        operator.gt,
+        operator.ge,
+        operator.lt,
+        operator.le,
+    ]
+    if is_cmp and isinstance(left, pd.DataFrame) and isinstance(right, pd.Series):
+        # in 2.0 silent alignment on comparisons was removed xref GH#28759
+        left, right = left.align(right, axis=1, copy=False)
+    elif is_cmp and isinstance(left, pd.Series) and isinstance(right, pd.DataFrame):
+        right, left = right.align(left, axis=1, copy=False)
+
     result = all_binary_operators(left, right)
     assert result.attrs == {"a": 1}