diff --git a/doc/source/whatsnew/v1.3.0.rst b/doc/source/whatsnew/v1.3.0.rst
index 645443c450146..c6e0e5bf2ffcd 100644
--- a/doc/source/whatsnew/v1.3.0.rst
+++ b/doc/source/whatsnew/v1.3.0.rst
@@ -679,6 +679,7 @@ Deprecations
 - Deprecated the ``convert_float`` optional argument in :func:`read_excel` and :meth:`ExcelFile.parse` (:issue:`41127`)
 - Deprecated behavior of :meth:`DatetimeIndex.union` with mixed timezones; in a future version both will be cast to UTC instead of object dtype (:issue:`39328`)
 - Deprecated using ``usecols`` with out of bounds indices for ``read_csv`` with ``engine="c"`` (:issue:`25623`)
+- Deprecated passing arguments as positional (except for ``"codes"``) in :meth:`MultiIndex.codes` (:issue:`41485`)
 - Deprecated passing arguments as positional in :meth:`Index.set_names` and :meth:`MultiIndex.set_names` (except for ``names``) (:issue:`41485`)
 - Deprecated passing arguments as positional in :meth:`DataFrame.clip` and :meth:`Series.clip` (other than ``"upper"`` and ``"lower"``) (:issue:`41485`)
 - Deprecated special treatment of lists with first element a Categorical in the :class:`DataFrame` constructor; pass as ``pd.DataFrame({col: categorical, ...})`` instead (:issue:`38845`)
diff --git a/pandas/core/indexes/multi.py b/pandas/core/indexes/multi.py
index 1362679ae0064..59882422f5439 100644
--- a/pandas/core/indexes/multi.py
+++ b/pandas/core/indexes/multi.py
@@ -991,6 +991,7 @@ def _set_codes(
 
         self._reset_cache()
 
+    @deprecate_nonkeyword_arguments(version=None, allowed_args=["self", "codes"])
     def set_codes(self, codes, level=None, inplace=None, verify_integrity: bool = True):
         """
         Set new codes on MultiIndex. Defaults to returning new index.
@@ -1058,7 +1059,7 @@ def set_codes(self, codes, level=None, inplace=None, verify_integrity: bool = Tr
             warnings.warn(
                 "inplace is deprecated and will be removed in a future version.",
                 FutureWarning,
-                stacklevel=2,
+                stacklevel=3,
             )
         else:
             inplace = False
diff --git a/pandas/tests/indexes/multi/test_get_set.py b/pandas/tests/indexes/multi/test_get_set.py
index e756f95bb2bc5..e806ee1751b00 100644
--- a/pandas/tests/indexes/multi/test_get_set.py
+++ b/pandas/tests/indexes/multi/test_get_set.py
@@ -449,3 +449,25 @@ def test_set_levels_pos_args_deprecation():
         names=["foo", "bar"],
     )
     tm.assert_index_equal(result, expected)
+
+
+def test_set_codes_pos_args_depreciation(idx):
+    # https://github.com/pandas-dev/pandas/issues/41485
+    msg = (
+        r"In a future version of pandas all arguments of MultiIndex.set_codes except "
+        r"for the argument 'codes' will be keyword-only"
+    )
+    with tm.assert_produces_warning(FutureWarning, match=msg):
+        result = idx.set_codes([[0, 0, 1, 2, 3, 3], [0, 1, 0, 1, 0, 1]], [0, 1])
+    expected = MultiIndex.from_tuples(
+        [
+            ("foo", "one"),
+            ("foo", "two"),
+            ("bar", "one"),
+            ("baz", "two"),
+            ("qux", "one"),
+            ("qux", "two"),
+        ],
+        names=["first", "second"],
+    )
+    tm.assert_index_equal(result, expected)