diff --git a/pandas/core/reshape/reshape.py b/pandas/core/reshape/reshape.py
index 0829aa8f5a509..622e3bd553f8c 100644
--- a/pandas/core/reshape/reshape.py
+++ b/pandas/core/reshape/reshape.py
@@ -653,7 +653,13 @@ def _convert_level_number(level_num, columns):
     # time to ravel the values
     new_data = {}
     level_vals = this.columns.levels[-1]
-    level_labels = sorted(set(this.columns.labels[-1]))
+    level_labels = list()
+    for label in this.columns.labels[-1]:
+        # GH 20945 if labels are not monotonic we were mangling
+        # alignment when moving to index; ensure we preserve order
+        if label not in level_labels:
+            level_labels.append(label)
+
     level_vals_used = level_vals[level_labels]
     levsize = len(level_labels)
     drop_cols = []
diff --git a/pandas/tests/frame/test_reshape.py b/pandas/tests/frame/test_reshape.py
index d89731dc09044..26bd72ebbf263 100644
--- a/pandas/tests/frame/test_reshape.py
+++ b/pandas/tests/frame/test_reshape.py
@@ -414,6 +414,25 @@ def test_stack_mixed_levels(self):
         assert_frame_equal(df3.stack(level=['animal', 0]),
                            animal_hair_stacked, check_names=False)
 
+    def test_stack_retains_index_order_non_monotonic(self):
+        # GH 20945
+        df = pd.DataFrame([
+            ['DIM', 'A', 1, 2, 3, 4],
+            ['DIM', 'B', 11, 22, 33, 44],
+        ])
+        df.columns = ["dim1", "dim2", 'c', 'b', 'a', 'd']
+        df.columns.name = 'foo'
+        df = df.set_index(["dim1", "dim2"])
+
+        expected_mi = pd.MultiIndex.from_product([['DIM'], ['c', 'b', 'a', 'd']])
+        expected_mi.names = ['dim1', 'foo']
+        expected = pd.DataFrame([[1, 11], [2, 22], [3, 33], [4, 44]],
+                                index=expected_mi, columns=['A', 'B'])
+        expected.columns.name = 'dim2'
+
+        result = df.unstack('dim2').stack(level=0)
+        tm.assert_frame_equal(result, expected)
+
     def test_stack_int_level_names(self):
         columns = MultiIndex.from_tuples(
             [('A', 'cat', 'long'), ('B', 'cat', 'long'),