diff --git a/doc/source/whatsnew/v1.2.4.rst b/doc/source/whatsnew/v1.2.4.rst
index 26d768f830830..9cef1307278e8 100644
--- a/doc/source/whatsnew/v1.2.4.rst
+++ b/doc/source/whatsnew/v1.2.4.rst
@@ -17,6 +17,7 @@ Fixed regressions
 
 - Fixed regression in :meth:`DataFrame.sum` when ``min_count`` greater than the :class:`DataFrame` shape was passed resulted in a ``ValueError`` (:issue:`39738`)
 - Fixed regression in :meth:`DataFrame.to_json` raising ``AttributeError`` when run on PyPy (:issue:`39837`)
+- Fixed regression in (in)equality comparison of ``pd.NaT`` with a non-datetimelike numpy array returning a scalar instead of an array (:issue:`40722`)
 - Fixed regression in :meth:`DataFrame.where` not returning a copy in the case of an all True condition (:issue:`39595`)
 - Fixed regression in :meth:`DataFrame.replace` raising ``IndexError`` when ``regex`` was a multi-key dictionary (:issue:`39338`)
 -
diff --git a/pandas/_libs/tslibs/nattype.pyx b/pandas/_libs/tslibs/nattype.pyx
index d86d3261d404e..0c598beb6ad16 100644
--- a/pandas/_libs/tslibs/nattype.pyx
+++ b/pandas/_libs/tslibs/nattype.pyx
@@ -127,6 +127,10 @@ cdef class _NaT(datetime):
                 result.fill(_nat_scalar_rules[op])
             elif other.dtype.kind == "O":
                 result = np.array([PyObject_RichCompare(self, x, op) for x in other])
+            elif op == Py_EQ:
+                result = np.zeros(other.shape, dtype=bool)
+            elif op == Py_NE:
+                result = np.ones(other.shape, dtype=bool)
             else:
                 return NotImplemented
             return result
diff --git a/pandas/tests/scalar/test_nat.py b/pandas/tests/scalar/test_nat.py
index 96aea4da9fac5..08c5ea706111a 100644
--- a/pandas/tests/scalar/test_nat.py
+++ b/pandas/tests/scalar/test_nat.py
@@ -590,6 +590,47 @@ def test_nat_comparisons_invalid(other_and_type, symbol_and_op):
         op(other, NaT)
 
 
+@pytest.mark.parametrize(
+    "other",
+    [
+        np.array(["foo"] * 2, dtype=object),
+        np.array([2, 3], dtype="int64"),
+        np.array([2.0, 3.5], dtype="float64"),
+    ],
+    ids=["str", "int", "float"],
+)
+def test_nat_comparisons_invalid_ndarray(other):
+    # GH#40722
+    expected = np.array([False, False])
+    result = NaT == other
+    tm.assert_numpy_array_equal(result, expected)
+    result = other == NaT
+    tm.assert_numpy_array_equal(result, expected)
+
+    expected = np.array([True, True])
+    result = NaT != other
+    tm.assert_numpy_array_equal(result, expected)
+    result = other != NaT
+    tm.assert_numpy_array_equal(result, expected)
+
+    for symbol, op in [
+        ("<=", operator.le),
+        ("<", operator.lt),
+        (">=", operator.ge),
+        (">", operator.gt),
+    ]:
+        msg = f"'{symbol}' not supported between"
+
+        with pytest.raises(TypeError, match=msg):
+            op(NaT, other)
+
+        if other.dtype == np.dtype("object"):
+            # uses the reverse operator, so symbol changes
+            msg = None
+        with pytest.raises(TypeError, match=msg):
+            op(other, NaT)
+
+
 def test_compare_date():
     # GH#39151 comparing NaT with date object is deprecated
     # See also: tests.scalar.timestamps.test_comparisons::test_compare_date