diff --git a/synapse/storage/databases/main/event_push_actions.py b/synapse/storage/databases/main/event_push_actions.py
index 3e26360c2c62..852e34796702 100644
--- a/synapse/storage/databases/main/event_push_actions.py
+++ b/synapse/storage/databases/main/event_push_actions.py
@@ -294,6 +294,22 @@ def __init__(
             self._background_backfill_thread_id,
         )
 
+        # Indexes which will be used to quickly make the thread_id column non-null.
+        self.db_pool.updates.register_background_index_update(
+            "event_push_actions_thread_id_null",
+            index_name="event_push_actions_thread_id_null",
+            table="event_push_actions",
+            columns=["thread_id"],
+            where_clause="thread_id IS NULL",
+        )
+        self.db_pool.updates.register_background_index_update(
+            "event_push_summary_thread_id_null",
+            index_name="event_push_summary_thread_id_null",
+            table="event_push_summary",
+            columns=["thread_id"],
+            where_clause="thread_id IS NULL",
+        )
+
         # Check ASAP (and then later, every 1s) to see if we have finished
         # background updates the event_push_actions and event_push_summary tables.
         self._clock.call_later(0.0, self._check_event_push_backfill_thread_id)
diff --git a/synapse/storage/schema/main/delta/73/06thread_notifications_thread_id_idx.sql b/synapse/storage/schema/main/delta/73/06thread_notifications_thread_id_idx.sql
new file mode 100644
index 000000000000..7983f9d4b196
--- /dev/null
+++ b/synapse/storage/schema/main/delta/73/06thread_notifications_thread_id_idx.sql
@@ -0,0 +1,20 @@
+/* Copyright 2022 The Matrix.org Foundation C.I.C
+ *
+ * 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 (ordering, update_name, progress_json, depends_on) VALUES
+  (7306, 'event_push_actions_thread_id_null', '{}', 'event_push_backfill_thread_id');
+
+INSERT INTO background_updates (ordering, update_name, progress_json, depends_on) VALUES
+  (7306, 'event_push_summary_thread_id_null', '{}', 'event_push_backfill_thread_id');