diff --git a/synapse/storage/background_updates.py b/synapse/storage/background_updates.py
index 003f5ba20..94b2bcc54 100644
--- a/synapse/storage/background_updates.py
+++ b/synapse/storage/background_updates.py
@@ -219,7 +219,7 @@ class BackgroundUpdateStore(SQLBaseStore):
         self._background_update_handlers[update_name] = update_handler
 
     def register_background_index_update(self, update_name, index_name,
-                                         table, columns):
+                                         table, columns, where_clause=None):
         """Helper for store classes to do a background index addition
 
         To use:
@@ -243,14 +243,20 @@ class BackgroundUpdateStore(SQLBaseStore):
             conc = True
         else:
             conc = False
+            # We don't use partial indices on SQLite as it wasn't introduced
+            # until 3.8, and wheezy has 3.7
+            where_clause = None
 
-        sql = "CREATE INDEX %(conc)s %(name)s ON %(table)s (%(columns)s)" \
-              % {
-                  "conc": "CONCURRENTLY" if conc else "",
-                  "name": index_name,
-                  "table": table,
-                  "columns": ", ".join(columns),
-              }
+        sql = (
+            "CREATE INDEX %(conc)s %(name)s ON %(table)s (%(columns)s)"
+            " %(where_clause)s"
+        ) % {
+            "conc": "CONCURRENTLY" if conc else "",
+            "name": index_name,
+            "table": table,
+            "columns": ", ".join(columns),
+            "where_clause": "WHERE " + where_clause if where_clause else ""
+        }
 
         def create_index_concurrently(conn):
             conn.rollback()
diff --git a/synapse/storage/event_push_actions.py b/synapse/storage/event_push_actions.py
index 51b13e949..efa1db3b9 100644
--- a/synapse/storage/event_push_actions.py
+++ b/synapse/storage/event_push_actions.py
@@ -36,7 +36,8 @@ class EventPushActionsStore(SQLBaseStore):
             self.EPA_HIGHLIGHT_INDEX,
             index_name="event_push_actions_u_highlight",
             table="event_push_actions",
-            columns=["user_id", "stream_ordering", "highlight"],
+            columns=["user_id", "stream_ordering"],
+            where_clause="highlight = 1",
         )
 
     def _set_push_actions_for_event_and_users_txn(self, txn, event, tuples):