diff --git a/doc/source/whatsnew/v1.3.0.rst b/doc/source/whatsnew/v1.3.0.rst
index 24cd41383e9d7..5436685c1f14f 100644
--- a/doc/source/whatsnew/v1.3.0.rst
+++ b/doc/source/whatsnew/v1.3.0.rst
@@ -692,9 +692,11 @@ Deprecations
 - Deprecated passing arguments (apart from ``value``) as positional in :meth:`DataFrame.fillna` and :meth:`Series.fillna` (:issue:`41485`)
 - Deprecated passing arguments as positional in :meth:`DataFrame.reset_index` (other than ``"level"``) and :meth:`Series.reset_index` (:issue:`41485`)
 - Deprecated construction of :class:`Series` or :class:`DataFrame` with ``DatetimeTZDtype`` data and ``datetime64[ns]`` dtype.  Use ``Series(data).dt.tz_localize(None)`` instead (:issue:`41555`,:issue:`33401`)
+- Deprecated passing arguments as positional in :meth:`DataFrame.set_axis` and :meth:`Series.set_axis` (other than ``"labels"``) (:issue:`41485`)
 - Deprecated passing arguments as positional in :meth:`DataFrame.where` and :meth:`Series.where` (other than ``"cond"`` and ``"other"``) (:issue:`41485`)
 -
 
+
 .. _whatsnew_130.deprecations.nuisance_columns:
 
 Deprecated Dropping Nuisance Columns in DataFrame Reductions and DataFrameGroupBy Operations
diff --git a/pandas/core/frame.py b/pandas/core/frame.py
index 75d2f4c591053..d2108fb901ca2 100644
--- a/pandas/core/frame.py
+++ b/pandas/core/frame.py
@@ -4703,6 +4703,7 @@ def set_axis(
     ) -> DataFrame | None:
         ...
 
+    @deprecate_nonkeyword_arguments(version=None, allowed_args=["self", "labels"])
     @Appender(
         """
         Examples
diff --git a/pandas/core/generic.py b/pandas/core/generic.py
index 8bbfa1f1db680..3e6642d3b1a72 100644
--- a/pandas/core/generic.py
+++ b/pandas/core/generic.py
@@ -9221,7 +9221,7 @@ def shift(
         else:
             new_ax = index.shift(periods, freq)
 
-        result = self.set_axis(new_ax, axis)
+        result = self.set_axis(new_ax, axis=axis)
         return result.__finalize__(self, method="shift")
 
     @final
diff --git a/pandas/core/series.py b/pandas/core/series.py
index 686e6966d8e24..5767d7bd1cd44 100644
--- a/pandas/core/series.py
+++ b/pandas/core/series.py
@@ -4483,6 +4483,7 @@ def set_axis(self, labels, *, inplace: Literal[True]) -> None:
     def set_axis(self, labels, axis: Axis = ..., inplace: bool = ...) -> Series | None:
         ...
 
+    @deprecate_nonkeyword_arguments(version=None, allowed_args=["self", "labels"])
     @Appender(
         """
         Examples
diff --git a/pandas/tests/frame/methods/test_set_axis.py b/pandas/tests/frame/methods/test_set_axis.py
index ee538e1d9d9ac..3284243ddac48 100644
--- a/pandas/tests/frame/methods/test_set_axis.py
+++ b/pandas/tests/frame/methods/test_set_axis.py
@@ -98,3 +98,26 @@ class TestSeriesSetAxis(SharedSetAxisTests):
     def obj(self):
         ser = Series(np.arange(4), index=[1, 3, 5, 7], dtype="int64")
         return ser
+
+
+def test_nonkeyword_arguments_deprecation_warning():
+    # https://github.com/pandas-dev/pandas/issues/41485
+    df = DataFrame({"a": [1, 2, 3]})
+    msg = (
+        r"In a future version of pandas all arguments of DataFrame\.set_axis "
+        r"except for the argument 'labels' will be keyword-only"
+    )
+    with tm.assert_produces_warning(FutureWarning, match=msg):
+        result = df.set_axis([1, 2, 4], 0)
+    expected = DataFrame({"a": [1, 2, 3]}, index=[1, 2, 4])
+    tm.assert_frame_equal(result, expected)
+
+    ser = Series([1, 2, 3])
+    msg = (
+        r"In a future version of pandas all arguments of Series\.set_axis "
+        r"except for the argument 'labels' will be keyword-only"
+    )
+    with tm.assert_produces_warning(FutureWarning, match=msg):
+        result = ser.set_axis([1, 2, 4], 0)
+    expected = Series([1, 2, 3], index=[1, 2, 4])
+    tm.assert_series_equal(result, expected)
diff --git a/pandas/tests/reshape/concat/test_categorical.py b/pandas/tests/reshape/concat/test_categorical.py
index a81085e083199..d8b5f19c6a745 100644
--- a/pandas/tests/reshape/concat/test_categorical.py
+++ b/pandas/tests/reshape/concat/test_categorical.py
@@ -148,8 +148,8 @@ def test_categorical_index_preserver(self):
         result = pd.concat([df2, df3])
         expected = pd.concat(
             [
-                df2.set_axis(df2.index.astype(object), 0),
-                df3.set_axis(df3.index.astype(object), 0),
+                df2.set_axis(df2.index.astype(object), axis=0),
+                df3.set_axis(df3.index.astype(object), axis=0),
             ]
         )
         tm.assert_frame_equal(result, expected)