BUG: CategoricalIndex.get_indexer issue with NaNs (#45361)

pandas/core/indexes/base.py

@@ -3696,6 +3696,7 @@ def get_indexer(
         tolerance=None,
     ) -> npt.NDArray[np.intp]:
         method = missing.clean_reindex_fill_method(method)
+        orig_target = target
         target = self._maybe_cast_listlike_indexer(target)
 
         self._check_indexing_method(method, limit, tolerance)
@@ -3718,9 +3719,17 @@ def get_indexer(
 
             indexer = self._engine.get_indexer(target.codes)
             if self.hasnans and target.hasnans:
+                # After _maybe_cast_listlike_indexer, target elements which do not
+                # belong to some category are changed to NaNs
+                # Mask to track actual NaN values compared to inserted NaN values
+                try:
+                    target_nans = isna(orig_target)
+                except NotImplementedError:
+                    target_nans = False
                 loc = self.get_loc(np.nan)
                 mask = target.isna()
-                indexer[mask] = loc
+                indexer[target_nans] = loc
+                indexer[mask & ~target_nans] = -1
             return indexer
 
         if is_categorical_dtype(target.dtype):

pandas/tests/indexes/categorical/test_indexing.py

@@ -298,6 +298,18 @@ def test_get_indexer_same_categories_different_order(self):
         expected = np.array([1, 1], dtype="intp")
         tm.assert_numpy_array_equal(result, expected)
 
+    def test_get_indexer_nans_in_index_and_target(self):
+        # GH 45361
+        ci = CategoricalIndex([1, 2, np.nan, 3])
+        other1 = [2, 3, 4, np.nan]
+        other2 = [1, 4, 2, 3]
+        res1 = ci.get_indexer(other1)
+        res2 = ci.get_indexer(other2)
+        expected1 = np.array([1, 3, -1, 2], dtype=np.intp)
+        expected2 = np.array([0, -1, 1, 3], dtype=np.intp)
+        tm.assert_numpy_array_equal(res1, expected1)
+        tm.assert_numpy_array_equal(res2, expected2)
+
 
 class TestWhere:
     def test_where(self, listlike_box):