diff --git a/featuretools/entityset/entity.py b/featuretools/entityset/entity.py
index 2e3f8e4305..7e07477af6 100644
--- a/featuretools/entityset/entity.py
+++ b/featuretools/entityset/entity.py
@@ -288,7 +288,7 @@ def query_by_values(self, instance_vals, variable_id=None, columns=None,
                 Data older than time_last by more than this will be ignored
 
         Returns:
-            pd.DataFrame : instances that match constraints
+            pd.DataFrame : instances that match constraints with ids in order of underlying dataframe
         """
         instance_vals = self._vals_to_series(instance_vals, variable_id)
 
@@ -309,8 +309,8 @@ def query_by_values(self, instance_vals, variable_id=None, columns=None,
             df.dropna(subset=[self.index], inplace=True)
 
         else:
-            df = self.df.merge(instance_vals.to_frame(variable_id),
-                               how="inner", on=variable_id)
+            df = self.df[self.df[variable_id].isin(instance_vals)]
+
             df = df.set_index(self.index, drop=False)
 
             # ensure filtered df has same categories as original
diff --git a/featuretools/tests/entityset_tests/test_entity.py b/featuretools/tests/entityset_tests/test_entity.py
index 8434b35f62..4d236ea63c 100644
--- a/featuretools/tests/entityset_tests/test_entity.py
+++ b/featuretools/tests/entityset_tests/test_entity.py
@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 from datetime import datetime
 
+import numpy as np
 import pandas as pd
 import pytest
 
@@ -95,3 +96,19 @@ def test_update_data(es):
     assert es["customers"].df["id"].iloc[0] == 0
     es["customers"].update_data(df.copy(deep=True), already_sorted=True)
     assert es["customers"].df["id"].iloc[0] == 2
+
+
+def test_query_by_values_returns_rows_in_given_order():
+    data = pd.DataFrame({
+        "id": [1, 2, 3, 4, 5],
+        "value": ["a", "c", "b", "a", "a"],
+        "time": [1000, 2000, 3000, 4000, 5000]
+    })
+
+    es = ft.EntitySet()
+    es = es.entity_from_dataframe(entity_id="test", dataframe=data, index="id",
+                                  time_index="time", variable_types={
+                                      "value": ft.variable_types.Categorical
+                                  })
+    query = es['test'].query_by_values(['b', 'a'], variable_id='value')
+    assert np.array_equal(query['id'], [1, 3, 4, 5])