diff --git a/doc/source/whatsnew/v1.3.0.rst b/doc/source/whatsnew/v1.3.0.rst
index fc49177a4736b..b019c5b3d30e8 100644
--- a/doc/source/whatsnew/v1.3.0.rst
+++ b/doc/source/whatsnew/v1.3.0.rst
@@ -412,6 +412,7 @@ Reshaping
 - Bug in :meth:`DataFrame.join` not assigning values correctly when having :class:`MultiIndex` where at least one dimension is from dtype ``Categorical`` with non-alphabetically sorted categories (:issue:`38502`)
 - :meth:`Series.value_counts` and :meth:`Series.mode` return consistent keys in original order (:issue:`12679`, :issue:`11227` and :issue:`39007`)
 - Bug in :meth:`DataFrame.apply` would give incorrect results when used with a string argument and ``axis=1`` when the axis argument was not supported and now raises a ``ValueError`` instead (:issue:`39211`)
+- Bug in :meth:`DataFrame.sort_values` not reshaping index correctly after sorting on columns, when ``ignore_index=True`` (:issue:`39464`)
 - Bug in :meth:`DataFrame.append` returning incorrect dtypes with combinations of ``ExtensionDtype`` dtypes (:issue:`39454`)
 
 Sparse
diff --git a/pandas/core/frame.py b/pandas/core/frame.py
index 57eb384d79868..6357b8feb348b 100644
--- a/pandas/core/frame.py
+++ b/pandas/core/frame.py
@@ -5560,7 +5560,9 @@ def sort_values(  # type: ignore[override]
         )
 
         if ignore_index:
-            new_data.set_axis(1, ibase.default_index(len(indexer)))
+            new_data.set_axis(
+                self._get_block_manager_axis(axis), ibase.default_index(len(indexer))
+            )
 
         result = self._constructor(new_data)
         if inplace:
diff --git a/pandas/tests/frame/methods/test_sort_values.py b/pandas/tests/frame/methods/test_sort_values.py
index 86c9e2f5ffe52..053684ba08484 100644
--- a/pandas/tests/frame/methods/test_sort_values.py
+++ b/pandas/tests/frame/methods/test_sort_values.py
@@ -579,6 +579,14 @@ def test_sort_values_item_cache(self, using_array_manager):
 
         assert df.iloc[0, 0] == df["A"][0]
 
+    def test_sort_values_reshaping(self):
+        # GH 39426
+        values = list(range(21))
+        expected = DataFrame([values], columns=values)
+        df = expected.sort_values(expected.index[0], axis=1, ignore_index=True)
+
+        tm.assert_frame_equal(df, expected)
+
 
 class TestDataFrameSortKey:  # test key sorting (issue 27237)
     def test_sort_values_inplace_key(self, sort_by_key):