diff --git a/doc/source/whatsnew/v1.4.0.rst b/doc/source/whatsnew/v1.4.0.rst
index 2c77b87f8efb6..9e5e2b5db94b9 100644
--- a/doc/source/whatsnew/v1.4.0.rst
+++ b/doc/source/whatsnew/v1.4.0.rst
@@ -914,6 +914,7 @@ Reshaping
 - Fixed metadata propagation in :meth:`Dataframe.apply` method, consequently fixing the same issue for :meth:`Dataframe.transform`, :meth:`Dataframe.nunique` and :meth:`Dataframe.mode` (:issue:`28283`)
 - Bug in :func:`concat` casting levels of :class:`MultiIndex` to float if the only consist of missing values (:issue:`44900`)
 - Bug in :meth:`DataFrame.stack` with ``ExtensionDtype`` columns incorrectly raising (:issue:`43561`)
+- Bug in :func:`merge` raising ``KeyError`` when joining over differently named indexes with on keywords (:issue:`45094`)
 - Bug in :meth:`Series.unstack` with object doing unwanted type inference on resulting columns (:issue:`44595`)
 - Bug in :class:`MultiIndex` failing join operations with overlapping ``IntervalIndex`` levels (:issue:`44096`)
 - Bug in :meth:`DataFrame.replace` and :meth:`Series.replace` results is different ``dtype`` based on ``regex`` parameter (:issue:`44864`)
diff --git a/pandas/core/reshape/merge.py b/pandas/core/reshape/merge.py
index 9a534ef7625a4..412cc5a8b43a3 100644
--- a/pandas/core/reshape/merge.py
+++ b/pandas/core/reshape/merge.py
@@ -820,6 +820,7 @@ def _maybe_restore_index_levels(self, result: DataFrame) -> None:
             if (
                 self.orig_left._is_level_reference(left_key)
                 and self.orig_right._is_level_reference(right_key)
+                and left_key == right_key
                 and name not in result.index.names
             ):
 
diff --git a/pandas/tests/reshape/merge/test_merge.py b/pandas/tests/reshape/merge/test_merge.py
index 4365f61860209..1249194d3a36d 100644
--- a/pandas/tests/reshape/merge/test_merge.py
+++ b/pandas/tests/reshape/merge/test_merge.py
@@ -2620,3 +2620,12 @@ def test_merge_outer_with_NaN(dtype):
         dtype=dtype,
     )
     tm.assert_frame_equal(result, expected)
+
+
+def test_merge_different_index_names():
+    # GH#45094
+    left = DataFrame({"a": [1]}, index=pd.Index([1], name="c"))
+    right = DataFrame({"a": [1]}, index=pd.Index([1], name="d"))
+    result = merge(left, right, left_on="c", right_on="d")
+    expected = DataFrame({"a_x": [1], "a_y": 1})
+    tm.assert_frame_equal(result, expected)