diff --git a/pandas/core/internals/blocks.py b/pandas/core/internals/blocks.py
index 953ccedaa5222..7f0915dbbaee4 100644
--- a/pandas/core/internals/blocks.py
+++ b/pandas/core/internals/blocks.py
@@ -426,7 +426,10 @@ def fillna(
         """
         inplace = validate_bool_kwarg(inplace, "inplace")
 
-        mask = isna(self.values)
+        isna_mask = isna(self.values)
+        value_mask = ~isna(value)
+        mask = isna_mask & value_mask
+
         mask, noop = validate_putmask(self.values, mask)
 
         if limit is not None:
diff --git a/pandas/io/json/_json.py b/pandas/io/json/_json.py
index fdeda868fdb5e..00160636aea34 100644
--- a/pandas/io/json/_json.py
+++ b/pandas/io/json/_json.py
@@ -924,7 +924,10 @@ def _try_convert_data(self, name, data, use_dtypes=True, convert_dates=True):
             if not self.dtype:
                 if all(notna(data)):
                     return data, False
-                return data.fillna(np.nan), True
+                data = data.where(notna(data), np.nan)
+                if isna(data).all():
+                    data = data.astype(np.float64)
+                return data, True
 
             # error: Non-overlapping identity check (left operand type:
             # "Union[ExtensionDtype, str, dtype[Any], Type[object],
diff --git a/pandas/tests/frame/methods/test_fillna.py b/pandas/tests/frame/methods/test_fillna.py
index b1ce511fc3e4c..0d0f47d58461b 100644
--- a/pandas/tests/frame/methods/test_fillna.py
+++ b/pandas/tests/frame/methods/test_fillna.py
@@ -153,6 +153,28 @@ def test_fillna_tzaware_different_column(self):
         )
         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])
diff --git a/pandas/tests/series/methods/test_fillna.py b/pandas/tests/series/methods/test_fillna.py
index 03e126587ce1a..53fcf47f47aa4 100644
--- a/pandas/tests/series/methods/test_fillna.py
+++ b/pandas/tests/series/methods/test_fillna.py
@@ -623,6 +623,19 @@ def test_fillna_numeric_inplace(self):
         expected = x.fillna(value=0)
         tm.assert_series_equal(y, 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