BUG: make pct_change can handle the anchored freq #28664

doc/source/whatsnew/v1.0.0.rst

@@ -370,6 +370,7 @@ Other
 - :meth:`DataFrame.to_csv` and :meth:`Series.to_csv` now support dicts as ``compression`` argument with key ``'method'`` being the compression method and others as additional compression options when the compression method is ``'zip'``. (:issue:`26023`)
 - Bug in :meth:`Series.diff` where a boolean series would incorrectly raise a ``TypeError`` (:issue:`17294`)
 - :meth:`Series.append` will no longer raise a ``TypeError`` when passed a tuple of ``Series`` (:issue:`28410`)
+- :meth:`Series.pct_change` will can handle duplicate axis (:issue:`28664`)
 - Fix corrupted error message when calling ``pandas.libs._json.encode()`` on a 0d array (:issue:`18878`)
 
 .. _whatsnew_1000.contributors:

pandas/core/generic.py

@@ -10413,6 +10413,7 @@ def pct_change(self, periods=1, fill_method="pad", limit=None, freq=None, **kwar
             data = self.fillna(method=fill_method, limit=limit, axis=axis)
 
         rs = data.div(data.shift(periods=periods, freq=freq, axis=axis, **kwargs)) - 1
+        rs = rs.loc[~rs.index.duplicated()]
         rs = rs.reindex_like(data)
         if freq is None:
             mask = isna(com.values_from_object(data))

pandas/tests/series/test_timeseries.py

@@ -373,6 +373,24 @@ def test_pct_change(self):
             rs, (filled / filled.shift(freq="5D") - 1).reindex_like(filled)
         )
 
+    @pytest.mark.parametrize("n_1", ["1", "15"])
+    @pytest.mark.parametrize("offset_1", ["D", "BM"])
+    @pytest.mark.parametrize("n_2", ["1", "3"])
+    @pytest.mark.parametrize("offset_2", ["D", "BM"])
+    def test_pct_change_with_duplicate_axis(self, n_1, offset_1, n_2, offset_2):
+        # GH 28664
+
+        freq_1 = n_1 + offset_1
+        freq_2 = n_2 + offset_2
+
+        s = Series([1, 2, 3, 4, 5] * 3, date_range("2019-09", periods=15, freq=freq_1))
+
+        result = s.pct_change(freq=freq_2)
+        expected = s / s.shift(freq=freq_2) - 1
+        expected = expected[expected.index.isin(s.index) & ~expected.index.duplicated()]
+
+        assert_series_equal(result, expected)
+
     def test_pct_change_shift_over_nas(self):
         s = Series([1.0, 1.5, np.nan, 2.5, 3.0])