diff --git a/pandas/core/indexes/base.py b/pandas/core/indexes/base.py
index b5900ead246f3..fac4940c0b573 100644
--- a/pandas/core/indexes/base.py
+++ b/pandas/core/indexes/base.py
@@ -4896,6 +4896,14 @@ def set_value(self, arr, key, value):
     @Appender(_index_shared_docs["get_indexer_non_unique"] % _index_doc_kwargs)
     def get_indexer_non_unique(self, target):
         target = ensure_index(target)
+
+        if target.is_boolean() and self.is_numeric():
+            # Treat boolean labels passed to a numeric index as not found. Without
+            # this fix False and True would be treated as 0 and 1 respectively.
+            # (GH #16877)
+            no_matches = -1 * np.ones(self.shape, dtype=np.intp)
+            return no_matches, no_matches
+
         pself, ptarget = self._maybe_promote(target)
         if pself is not self or ptarget is not target:
             return pself.get_indexer_non_unique(ptarget)
diff --git a/pandas/tests/indexes/test_base.py b/pandas/tests/indexes/test_base.py
index 2e3a70e8c2215..ba2ac5d2e07b2 100644
--- a/pandas/tests/indexes/test_base.py
+++ b/pandas/tests/indexes/test_base.py
@@ -1236,14 +1236,25 @@ def test_get_indexer_strings_raises(self):
                 ["a", "b", "c", "d"], method="pad", tolerance=[2, 2, 2, 2]
             )
 
-    @pytest.mark.parametrize("idx_class", [Int64Index, RangeIndex, Float64Index])
-    def test_get_indexer_numeric_index_boolean_target(self, idx_class):
+    @pytest.mark.parametrize(
+        "idx_class", [Int64Index, RangeIndex, Float64Index, UInt64Index]
+    )
+    @pytest.mark.parametrize("method", ["get_indexer", "get_indexer_non_unique"])
+    def test_get_indexer_numeric_index_boolean_target(self, method, idx_class):
         # GH 16877
 
         numeric_index = idx_class(RangeIndex(4))
-        result = numeric_index.get_indexer([True, False, True])
+        other = Index([True, False, True])
+
+        result = getattr(numeric_index, method)(other)
         expected = np.array([-1, -1, -1], dtype=np.intp)
-        tm.assert_numpy_array_equal(result, expected)
+        if method == "get_indexer":
+            tm.assert_numpy_array_equal(result, expected)
+        else:
+            expected = np.array([-1, -1, -1, -1], dtype=np.intp)
+
+            tm.assert_numpy_array_equal(result[0], expected)
+            tm.assert_numpy_array_equal(result[1], expected)
 
     def test_get_indexer_with_NA_values(
         self, unique_nulls_fixture, unique_nulls_fixture2