diff --git a/synapse/storage/event_push_actions.py b/synapse/storage/event_push_actions.py
index 9cd923eb93e1..7de3e8c58cbf 100644
--- a/synapse/storage/event_push_actions.py
+++ b/synapse/storage/event_push_actions.py
@@ -39,6 +39,14 @@ def __init__(self, hs):
             columns=["user_id", "stream_ordering"],
         )
 
+        self.register_background_index_update(
+            "event_push_actions_highlights_index",
+            index_name="event_push_actions_highlights_index",
+            table="event_push_actions",
+            columns=["user_id", "room_id", "topological_ordering", "stream_ordering"],
+            where_clause="highlight=1"
+        )
+
     def _set_push_actions_for_event_and_users_txn(self, txn, event, tuples):
         """
         Args:
@@ -88,8 +96,11 @@ def _get_unread_event_push_actions_by_room(txn):
                 topological_ordering, stream_ordering
             )
 
+            # First get number of notifications.
+            # We don't need to put a notif=1 clause as all rows always have
+            # notif=1
             sql = (
-                "SELECT sum(notif), sum(highlight)"
+                "SELECT count(*)"
                 " FROM event_push_actions ea"
                 " WHERE"
                 " user_id = ?"
@@ -99,13 +110,27 @@ def _get_unread_event_push_actions_by_room(txn):
 
             txn.execute(sql, (user_id, room_id))
             row = txn.fetchone()
-            if row:
-                return {
-                    "notify_count": row[0] or 0,
-                    "highlight_count": row[1] or 0,
-                }
-            else:
-                return {"notify_count": 0, "highlight_count": 0}
+            notify_count = row[0] if row else 0
+
+            # Now get the number of highlights
+            sql = (
+                "SELECT count(*)"
+                " FROM event_push_actions ea"
+                " WHERE"
+                " highlight = 1"
+                " AND user_id = ?"
+                " AND room_id = ?"
+                " AND %s"
+            ) % (lower_bound(token, self.database_engine, inclusive=False),)
+
+            txn.execute(sql, (user_id, room_id))
+            row = txn.fetchone()
+            highlight_count = row[0] if row else 0
+
+            return {
+                "notify_count": notify_count,
+                "highlight_count": highlight_count,
+            }
 
         ret = yield self.runInteraction(
             "get_unread_event_push_actions_by_room",
diff --git a/synapse/storage/schema/delta/39/event_push_index.sql b/synapse/storage/schema/delta/39/event_push_index.sql
new file mode 100644
index 000000000000..de2ad93e5cdc
--- /dev/null
+++ b/synapse/storage/schema/delta/39/event_push_index.sql
@@ -0,0 +1,17 @@
+/* Copyright 2016 OpenMarket Ltd
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+INSERT INTO background_updates (update_name, progress_json) VALUES
+  ('event_push_actions_highlights_index', '{}');