diff --git a/doc/source/whatsnew/v2.1.0.rst b/doc/source/whatsnew/v2.1.0.rst
index ed8646bafc4db..415b9e9c21f52 100644
--- a/doc/source/whatsnew/v2.1.0.rst
+++ b/doc/source/whatsnew/v2.1.0.rst
@@ -318,6 +318,7 @@ Deprecations
 - Deprecated the ``axis`` keyword in :meth:`DataFrame.ewm`, :meth:`Series.ewm`, :meth:`DataFrame.rolling`, :meth:`Series.rolling`, :meth:`DataFrame.expanding`, :meth:`Series.expanding` (:issue:`51778`)
 - Deprecated the ``axis`` keyword in :meth:`DataFrame.resample`, :meth:`Series.resample` (:issue:`51778`)
 - Deprecated the behavior of :func:`concat` with both ``len(keys) != len(objs)``, in a future version this will raise instead of truncating to the shorter of the two sequences (:issue:`43485`)
+- Deprecated the behavior of :meth:`Series.argsort` in the presence of NA values; in a future version these will be sorted at the end instead of giving -1 (:issue:`54219`)
 - Deprecated the default of ``observed=False`` in :meth:`DataFrame.groupby` and :meth:`Series.groupby`; this will default to ``True`` in a future version (:issue:`43999`)
 - Deprecating pinning ``group.name`` to each group in :meth:`SeriesGroupBy.aggregate` aggregations; if your operation requires utilizing the groupby keys, iterate over the groupby object instead (:issue:`41090`)
 - Deprecated the 'axis' keyword in :meth:`.GroupBy.idxmax`, :meth:`.GroupBy.idxmin`, :meth:`.GroupBy.fillna`, :meth:`.GroupBy.take`, :meth:`.GroupBy.skew`, :meth:`.GroupBy.rank`, :meth:`.GroupBy.cumprod`, :meth:`.GroupBy.cumsum`, :meth:`.GroupBy.cummax`, :meth:`.GroupBy.cummin`, :meth:`.GroupBy.pct_change`, :meth:`GroupBy.diff`, :meth:`.GroupBy.shift`, and :meth:`DataFrameGroupBy.corrwith`; for ``axis=1`` operate on the underlying :class:`DataFrame` instead (:issue:`50405`, :issue:`51046`)
diff --git a/pandas/core/series.py b/pandas/core/series.py
index b7445bf158b90..b376ee46b7949 100644
--- a/pandas/core/series.py
+++ b/pandas/core/series.py
@@ -3946,6 +3946,13 @@ def argsort(
         mask = isna(values)
 
         if mask.any():
+            warnings.warn(
+                "The behavior of Series.argsort in the presence of NA values is "
+                "deprecated. In a future version, NA values will be ordered "
+                "last instead of set to -1.",
+                FutureWarning,
+                stacklevel=find_stack_level(),
+            )
             result = np.full(len(self), -1, dtype=np.intp)
             notmask = ~mask
             result[notmask] = np.argsort(values[notmask], kind=kind)
diff --git a/pandas/tests/extension/base/methods.py b/pandas/tests/extension/base/methods.py
index bc79db3d18ad7..7a5c07e736811 100644
--- a/pandas/tests/extension/base/methods.py
+++ b/pandas/tests/extension/base/methods.py
@@ -107,7 +107,9 @@ def test_argsort_missing_array(self, data_missing_for_sorting):
         tm.assert_numpy_array_equal(result, expected)
 
     def test_argsort_missing(self, data_missing_for_sorting):
-        result = pd.Series(data_missing_for_sorting).argsort()
+        msg = "The behavior of Series.argsort in the presence of NA values"
+        with tm.assert_produces_warning(FutureWarning, match=msg):
+            result = pd.Series(data_missing_for_sorting).argsort()
         expected = pd.Series(np.array([1, -1, 0], dtype=np.intp))
         self.assert_series_equal(result, expected)
 
diff --git a/pandas/tests/series/methods/test_argsort.py b/pandas/tests/series/methods/test_argsort.py
index e1d64795e235d..8549ecb99d061 100644
--- a/pandas/tests/series/methods/test_argsort.py
+++ b/pandas/tests/series/methods/test_argsort.py
@@ -21,7 +21,11 @@ def test_argsort_numpy(self, datetime_series):
         ts = ser.copy()
         ts[::2] = np.NaN
 
-        result = func(ts)[1::2]
+        msg = "The behavior of Series.argsort in the presence of NA values"
+        with tm.assert_produces_warning(
+            FutureWarning, match=msg, check_stacklevel=False
+        ):
+            result = func(ts)[1::2]
         expected = func(np.array(ts.dropna()))
 
         tm.assert_numpy_array_equal(result.values, expected, check_dtype=False)
@@ -41,7 +45,9 @@ def test_argsort(self, datetime_series):
         expected = Series(range(5), dtype=np.intp)
         tm.assert_series_equal(result, expected)
 
-        result = shifted.argsort()
+        msg = "The behavior of Series.argsort in the presence of NA values"
+        with tm.assert_produces_warning(FutureWarning, match=msg):
+            result = shifted.argsort()
         expected = Series(list(range(4)) + [-1], dtype=np.intp)
         tm.assert_series_equal(result, expected)