BUG GH#40498 Fillna other missing values not modified

pandas/core/generic.py

@@ -6275,11 +6275,13 @@ def fillna(
         else:
             if self.ndim == 1:
                 if isinstance(value, (dict, ABCSeries)):
-                    value = create_series_with_explicit_dtype(
+                    value_map = create_series_with_explicit_dtype(
                         value, dtype_if_empty=object
                     )
-                    value = value.reindex(self.index, copy=False)
-                    value = value._values
+                    value = self.copy()
+                    modification_index = value.index.intersection(value_map.index)
+                    if not modification_index.empty:
+                        value.loc[modification_index] = value_map[modification_index]
                 elif not is_list_like(value):
                     pass
                 else:

pandas/tests/frame/methods/test_fillna.py

@@ -153,6 +153,48 @@ def test_fillna_tzaware_different_column(self):
         )
         tm.assert_frame_equal(result, expected)
 
+    def test_null_value_replacement(self):
+        # GH$40498
+        df = DataFrame(
+            {
+                "A": [1, 2, None, 4],
+                "B": [2, None, 6, 8],
+            }
+        )
+        value = np.nan
+        result = df.fillna(value)
+
+        expected = DataFrame(
+            {
+                "A": [1, 2, np.nan, 4],
+                "B": [2, np.nan, 6, 8],
+            }
+        )
+
+        tm.assert_frame_equal(result, expected)
+
+    def test_other_missing_values_not_modified(
+        self, unique_nulls_fixture, unique_nulls_fixture2
+    ):
+        # GH#40498
+        df = DataFrame(
+            {
+                "A": [1, unique_nulls_fixture, unique_nulls_fixture2, "four"],
+                "B": [2, unique_nulls_fixture, unique_nulls_fixture2, "eight"],
+            }
+        )
+        value = {"A": {1: 0}, "B": {2: 0}}
+        result = df.fillna(value)
+
+        expected = DataFrame(
+            {
+                "A": [1, 0, unique_nulls_fixture2, "four"],
+                "B": [2, unique_nulls_fixture, 0, "eight"],
+            }
+        )
+
+        tm.assert_frame_equal(result, expected)
+
     def test_na_actions_categorical(self):
 
         cat = Categorical([1, 2, 3, np.nan], categories=[1, 2, 3])

pandas/tests/series/methods/test_fillna.py

@@ -623,6 +623,30 @@ def test_fillna_numeric_inplace(self):
         expected = x.fillna(value=0)
         tm.assert_series_equal(y, expected)
 
+    def test_fillna_null_value_replacement(self):
+        # GH#40498
+        ser = Series([None])
+
+        value = np.nan
+        result = ser.fillna(value)
+
+        expected = Series([np.nan])
+
+        tm.assert_series_equal(result, expected)
+
+    def test_fillna_other_missing_values_not_modified(
+        self, unique_nulls_fixture, unique_nulls_fixture2
+    ):
+        # GH#40498
+        ser = Series([1, unique_nulls_fixture, unique_nulls_fixture2, "four"])
+
+        value = {2: 0}
+        result = ser.fillna(value)
+
+        expected = Series([1, unique_nulls_fixture, 0, "four"])
+
+        tm.assert_series_equal(result, expected)
+
     # ---------------------------------------------------------------
     # CategoricalDtype