diff --git a/doc/source/whatsnew/v3.0.0.rst b/doc/source/whatsnew/v3.0.0.rst
index ec5027840dfd5..bdcafb1f789fe 100644
--- a/doc/source/whatsnew/v3.0.0.rst
+++ b/doc/source/whatsnew/v3.0.0.rst
@@ -942,6 +942,7 @@ Other
 - Bug in :meth:`Series.replace` and :meth:`DataFrame.replace` inconsistently replacing matching instances when ``regex=True`` and missing values are present. (:issue:`56599`)
 - Bug in :meth:`Series.replace` and :meth:`DataFrame.replace` throwing ``ValueError`` when ``regex=True`` and all NA values. (:issue:`60688`)
 - Bug in :meth:`Series.to_string` when series contains complex floats with exponents (:issue:`60405`)
+- Bug in :meth:`pandas.testing.assert_series_equal` incorrectly failing when comparing :class:`Categorical` series with null values and different category orders when ``check_category_order=False`` (:issue:`62008`)
 - Bug in :meth:`read_csv` where chained fsspec TAR file and ``compression="infer"`` fails with ``tarfile.ReadError`` (:issue:`60028`)
 - Bug in Dataframe Interchange Protocol implementation was returning incorrect results for data buffers' associated dtype, for string and datetime columns (:issue:`54781`)
 - Bug in ``Series.list`` methods not preserving the original :class:`Index`. (:issue:`58425`)
diff --git a/pandas/_testing/asserters.py b/pandas/_testing/asserters.py
index daa5187cdb636..f7d3caae83e75 100644
--- a/pandas/_testing/asserters.py
+++ b/pandas/_testing/asserters.py
@@ -495,8 +495,8 @@ def assert_categorical_equal(
             lc, rc = left.categories, right.categories
         assert_index_equal(lc, rc, obj=f"{obj}.categories", exact=exact)
         assert_index_equal(
-            left.categories.take(left.codes),
-            right.categories.take(right.codes),
+            left.categories.take(left.codes, allow_fill=True, fill_value=np.nan),
+            right.categories.take(right.codes, allow_fill=True, fill_value=np.nan),
             obj=f"{obj}.values",
             exact=exact,
         )
diff --git a/pandas/tests/util/test_assert_series_equal.py b/pandas/tests/util/test_assert_series_equal.py
index 8c9fff8e6ae2d..20276c37d30d2 100644
--- a/pandas/tests/util/test_assert_series_equal.py
+++ b/pandas/tests/util/test_assert_series_equal.py
@@ -507,3 +507,19 @@ def test_assert_series_equal_check_exact_index_default(left_idx, right_idx):
     ser2 = Series(np.zeros(6, dtype=int), right_idx)
     tm.assert_series_equal(ser1, ser2)
     tm.assert_frame_equal(ser1.to_frame(), ser2.to_frame())
+
+
+def test_assert_series_equal_categorical_nulls_different_order():
+    # https://github.com/pandas-dev/pandas/issues/62008
+    values = ["B", np.nan, "D"]
+    categorical_left = ["B", "D"]
+    categorical_right = categorical_left[::-1]  # Different Order
+
+    left = Series(Categorical(values, categories=categorical_left))
+    right = Series(Categorical(values, categories=categorical_right))
+
+    tm.assert_series_equal(left, right, check_category_order=False)
+
+    msg = "Categorical.categories are different"
+    with pytest.raises(AssertionError, match=msg):
+        tm.assert_series_equal(left, right, check_category_order=True)