diff --git a/pandas/core/index.py b/pandas/core/index.py
index 81602d5240a08..da4defcecaa99 100644
--- a/pandas/core/index.py
+++ b/pandas/core/index.py
@@ -2133,6 +2133,12 @@ def isin(self, values):
         return lib.ismember_nans(self._array_values(), value_set,
                                  isnull(list(value_set)).any())
 
+    def get_indexer(self, values, method=None, limit=None):
+        result = super(Float64Index, self).get_indexer(values, method=method,
+                                                       limit=limit)
+        result[result == -1] = self._nan_idxs
+        return result
+
 
 class MultiIndex(Index):
 
diff --git a/pandas/tests/test_index.py b/pandas/tests/test_index.py
index a8486beb57042..b7263cc96855c 100644
--- a/pandas/tests/test_index.py
+++ b/pandas/tests/test_index.py
@@ -1049,6 +1049,18 @@ def test_astype_from_object(self):
         tm.assert_equal(result.dtype, expected.dtype)
         tm.assert_index_equal(result, expected)
 
+    def test_get_indexer_nans(self):
+        index = Index([1, 2, np.nan])
+        result = index.get_indexer([np.nan])
+        np.testing.assert_array_equal(result, np.array([2]))
+
+        index = Index([1, np.nan, 2, np.nan])
+        with tm.assertRaisesRegexp(InvalidIndexError, 'Reindexing.*valid.*'):
+            index.get_indexer([np.nan])
+
+        index = Index([1, np.nan, 2])
+        result = index.get_indexer([np.nan, np.nan])
+        np.testing.assert_array_equal(result, np.array([1, 1]))
 
 class TestInt64Index(tm.TestCase):
     _multiprocess_can_split_ = True