diff --git a/doc/source/whatsnew/v3.0.0.rst b/doc/source/whatsnew/v3.0.0.rst
index a619b08a8676f..bfaeefbdcfa72 100644
--- a/doc/source/whatsnew/v3.0.0.rst
+++ b/doc/source/whatsnew/v3.0.0.rst
@@ -1149,6 +1149,7 @@ Other
 - Bug in ``divmod`` and ``rdivmod`` with :class:`DataFrame`, :class:`Series`, and :class:`Index` with ``bool`` dtypes failing to raise, which was inconsistent with ``__floordiv__`` behavior (:issue:`46043`)
 - Bug in printing a :class:`DataFrame` with a :class:`DataFrame` stored in :attr:`DataFrame.attrs` raised a ``ValueError`` (:issue:`60455`)
 - Bug in printing a :class:`Series` with a :class:`DataFrame` stored in :attr:`Series.attrs` raised a ``ValueError`` (:issue:`60568`)
+- Deprecated the keyword ``check_datetimelike_compat`` in :meth:`testing.assert_frame_equal` and :meth:`testing.assert_series_equal` (:issue:`55638`)
 - Fixed bug where the :class:`DataFrame` constructor misclassified array-like objects with a ``.name`` attribute as :class:`Series` or :class:`Index` (:issue:`61443`)
 - Fixed regression in :meth:`DataFrame.from_records` not initializing subclasses properly (:issue:`57008`)
 
diff --git a/pandas/_testing/asserters.py b/pandas/_testing/asserters.py
index daa5187cdb636..1e03d60041875 100644
--- a/pandas/_testing/asserters.py
+++ b/pandas/_testing/asserters.py
@@ -7,6 +7,7 @@
     NoReturn,
     cast,
 )
+import warnings
 
 import numpy as np
 
@@ -15,6 +16,8 @@
 from pandas._libs.sparse import SparseIndex
 import pandas._libs.testing as _testing
 from pandas._libs.tslibs.np_datetime import compare_mismatched_resolutions
+from pandas.errors import Pandas4Warning
+from pandas.util._decorators import deprecate_kwarg
 
 from pandas.core.dtypes.common import (
     is_bool,
@@ -843,6 +846,7 @@ def assert_extension_array_equal(
 
 
 # This could be refactored to use the NDFrame.equals method
+@deprecate_kwarg(Pandas4Warning, "check_datetimelike_compat", new_arg_name=None)
 def assert_series_equal(
     left,
     right,
@@ -897,6 +901,9 @@ def assert_series_equal(
 
     check_datetimelike_compat : bool, default False
         Compare datetime-like which is comparable ignoring dtype.
+
+        .. deprecated:: 3.0
+
     check_categorical : bool, default True
         Whether to compare internal Categorical exactly.
     check_category_order : bool, default True
@@ -1132,6 +1139,7 @@ def assert_series_equal(
 
 
 # This could be refactored to use the NDFrame.equals method
+@deprecate_kwarg(Pandas4Warning, "check_datetimelike_compat", new_arg_name=None)
 def assert_frame_equal(
     left,
     right,
@@ -1194,6 +1202,9 @@ def assert_frame_equal(
             ``check_exact``, ``rtol`` and ``atol`` are specified.
     check_datetimelike_compat : bool, default False
         Compare datetime-like which is comparable ignoring dtype.
+
+        .. deprecated:: 3.0
+
     check_categorical : bool, default True
         Whether to compare internal Categorical exactly.
     check_like : bool, default False
@@ -1320,22 +1331,28 @@ def assert_frame_equal(
             # use check_index=False, because we do not want to run
             # assert_index_equal for each column,
             # as we already checked it for the whole dataframe before.
-            assert_series_equal(
-                lcol,
-                rcol,
-                check_dtype=check_dtype,
-                check_index_type=check_index_type,
-                check_exact=check_exact,
-                check_names=check_names,
-                check_datetimelike_compat=check_datetimelike_compat,
-                check_categorical=check_categorical,
-                check_freq=check_freq,
-                obj=f'{obj}.iloc[:, {i}] (column name="{col}")',
-                rtol=rtol,
-                atol=atol,
-                check_index=False,
-                check_flags=False,
-            )
+            with warnings.catch_warnings():
+                warnings.filterwarnings(
+                    "ignore",
+                    message="the 'check_datetimelike_compat' keyword",
+                    category=Pandas4Warning,
+                )
+                assert_series_equal(
+                    lcol,
+                    rcol,
+                    check_dtype=check_dtype,
+                    check_index_type=check_index_type,
+                    check_exact=check_exact,
+                    check_names=check_names,
+                    check_datetimelike_compat=check_datetimelike_compat,
+                    check_categorical=check_categorical,
+                    check_freq=check_freq,
+                    obj=f'{obj}.iloc[:, {i}] (column name="{col}")',
+                    rtol=rtol,
+                    atol=atol,
+                    check_index=False,
+                    check_flags=False,
+                )
 
 
 def assert_equal(left, right, **kwargs) -> None:
diff --git a/pandas/tests/util/test_assert_frame_equal.py b/pandas/tests/util/test_assert_frame_equal.py
index ea954756d63c8..8711365a19214 100644
--- a/pandas/tests/util/test_assert_frame_equal.py
+++ b/pandas/tests/util/test_assert_frame_equal.py
@@ -1,5 +1,7 @@
 import pytest
 
+from pandas.errors import Pandas4Warning
+
 import pandas as pd
 from pandas import DataFrame
 import pandas._testing as tm
@@ -395,3 +397,19 @@ def test_assert_frame_equal_set_mismatch():
     msg = r'DataFrame.iloc\[:, 0\] \(column name="set_column"\) values are different'
     with pytest.raises(AssertionError, match=msg):
         tm.assert_frame_equal(df1, df2)
+
+
+def test_datetimelike_compat_deprecated():
+    # GH#55638
+    df = DataFrame({"a": [1]})
+
+    msg = "the 'check_datetimelike_compat' keyword is deprecated"
+    with tm.assert_produces_warning(Pandas4Warning, match=msg):
+        tm.assert_frame_equal(df, df, check_datetimelike_compat=True)
+    with tm.assert_produces_warning(Pandas4Warning, match=msg):
+        tm.assert_frame_equal(df, df, check_datetimelike_compat=False)
+
+    with tm.assert_produces_warning(Pandas4Warning, match=msg):
+        tm.assert_series_equal(df["a"], df["a"], check_datetimelike_compat=True)
+    with tm.assert_produces_warning(Pandas4Warning, match=msg):
+        tm.assert_series_equal(df["a"], df["a"], check_datetimelike_compat=False)