diff --git a/pandas/tests/dtypes/test_missing.py b/pandas/tests/dtypes/test_missing.py
index eeddf443dba86..94707dc2e68c5 100644
--- a/pandas/tests/dtypes/test_missing.py
+++ b/pandas/tests/dtypes/test_missing.py
@@ -9,6 +9,7 @@
 
 from pandas._libs import missing as libmissing
 from pandas._libs.tslibs import iNaT
+from pandas.compat import is_numpy_dev
 
 from pandas.core.dtypes.common import (
     is_float,
@@ -460,7 +461,7 @@ def test_array_equivalent_series(val):
     cm = (
         # stacklevel is chosen to make sense when called from .equals
         tm.assert_produces_warning(FutureWarning, match=msg, check_stacklevel=False)
-        if isinstance(val, str)
+        if isinstance(val, str) and not is_numpy_dev
         else nullcontext()
     )
     with cm:
diff --git a/pandas/tests/frame/methods/test_compare.py b/pandas/tests/frame/methods/test_compare.py
index 2c47285d7c507..455acde1af684 100644
--- a/pandas/tests/frame/methods/test_compare.py
+++ b/pandas/tests/frame/methods/test_compare.py
@@ -1,6 +1,8 @@
 import numpy as np
 import pytest
 
+from pandas.compat import is_numpy_dev
+
 import pandas as pd
 import pandas._testing as tm
 
@@ -257,8 +259,13 @@ def test_compare_ea_and_np_dtype(val1, val2):
             ("b", "other"): np.nan,
         }
     )
-    result = df1.compare(df2, keep_shape=True)
-    tm.assert_frame_equal(result, expected)
+    if val1 is pd.NA and is_numpy_dev:
+        # can't compare with numpy array if it contains pd.NA
+        with pytest.raises(TypeError, match="boolean value of NA is ambiguous"):
+            result = df1.compare(df2, keep_shape=True)
+    else:
+        result = df1.compare(df2, keep_shape=True)
+        tm.assert_frame_equal(result, expected)
 
 
 @pytest.mark.parametrize(
diff --git a/pandas/tests/indexes/object/test_indexing.py b/pandas/tests/indexes/object/test_indexing.py
index a33173dc83569..87d3afc77d556 100644
--- a/pandas/tests/indexes/object/test_indexing.py
+++ b/pandas/tests/indexes/object/test_indexing.py
@@ -114,6 +114,13 @@ def test_get_indexer_non_unique_np_nats(self, np_nat_fixture, np_nat_fixture2):
             tm.assert_numpy_array_equal(missing, expected_missing)
         # dt64nat vs td64nat
         else:
+            try:
+                np_nat_fixture == np_nat_fixture2
+            except (TypeError, OverflowError):
+                # Numpy will raise on uncomparable types, like
+                # np.datetime64('NaT', 'Y') and np.datetime64('NaT', 'ps')
+                # https://github.com/numpy/numpy/issues/22762
+                return
             index = Index(
                 np.array(
                     [
diff --git a/pandas/tests/series/methods/test_equals.py b/pandas/tests/series/methods/test_equals.py
index 22e27c271df88..9278d1b51e1aa 100644
--- a/pandas/tests/series/methods/test_equals.py
+++ b/pandas/tests/series/methods/test_equals.py
@@ -5,6 +5,7 @@
 import pytest
 
 from pandas._libs.missing import is_matching_na
+from pandas.compat import is_numpy_dev
 
 from pandas.core.dtypes.common import is_float
 
@@ -50,7 +51,7 @@ def test_equals_list_array(val):
 
     cm = (
         tm.assert_produces_warning(FutureWarning, check_stacklevel=False)
-        if isinstance(val, str)
+        if isinstance(val, str) and not is_numpy_dev
         else nullcontext()
     )
     with cm: