diff --git a/changelog.d/13802.misc b/changelog.d/13802.misc
new file mode 100644
index 000000000..0d5507132
--- /dev/null
+++ b/changelog.d/13802.misc
@@ -0,0 +1 @@
+Use partial indices on SQLite.
diff --git a/synapse/storage/background_updates.py b/synapse/storage/background_updates.py
index 555b4e77d..cf1eabc43 100644
--- a/synapse/storage/background_updates.py
+++ b/synapse/storage/background_updates.py
@@ -581,9 +581,6 @@ class BackgroundUpdater:
         def create_index_sqlite(conn: Connection) -> None:
             # Sqlite doesn't support concurrent creation of indexes.
             #
-            # We don't use partial indices on SQLite as it wasn't introduced
-            # until 3.8, and wheezy and CentOS 7 have 3.7
-            #
             # We assume that sqlite doesn't give us invalid indices; however
             # we may still end up with the index existing but the
             # background_updates not having been recorded if synapse got shut
@@ -591,12 +588,13 @@ class BackgroundUpdater:
             # has supported CREATE TABLE|INDEX IF NOT EXISTS since 3.3.0.)
             sql = (
                 "CREATE %(unique)s INDEX IF NOT EXISTS %(name)s ON %(table)s"
-                " (%(columns)s)"
+                " (%(columns)s) %(where_clause)s"
             ) % {
                 "unique": "UNIQUE" if unique else "",
                 "name": index_name,
                 "table": table,
                 "columns": ", ".join(columns),
+                "where_clause": "WHERE " + where_clause if where_clause else "",
             }
 
             c = conn.cursor()
diff --git a/synapse/storage/databases/main/event_push_actions.py b/synapse/storage/databases/main/event_push_actions.py
index f4a07de2a..3a3fb8c50 100644
--- a/synapse/storage/databases/main/event_push_actions.py
+++ b/synapse/storage/databases/main/event_push_actions.py
@@ -1255,7 +1255,6 @@ class EventPushActionsStore(EventPushActionsWorkerStore):
             table="event_push_actions",
             columns=["highlight", "stream_ordering"],
             where_clause="highlight=0",
-            psql_only=True,
         )
 
     async def get_push_actions_for_user(
diff --git a/synapse/storage/schema/main/delta/72/09partial_indices.sql.sqlite b/synapse/storage/schema/main/delta/72/09partial_indices.sql.sqlite
new file mode 100644
index 000000000..c8dfdf021
--- /dev/null
+++ b/synapse/storage/schema/main/delta/72/09partial_indices.sql.sqlite
@@ -0,0 +1,56 @@
+/* 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.
+ */
+ 
+-- SQLite needs to rebuild indices which use partial indices on Postgres, but
+-- previously did not use them on SQLite.
+
+-- Drop each index that was added with register_background_index_update AND specified
+-- a where_clause (that existed before this delta).
+
+-- From events_bg_updates.py
+DROP INDEX IF EXISTS event_contains_url_index;
+-- There is also a redactions_censored_redacts index, but that gets dropped.
+DROP INDEX IF EXISTS redactions_have_censored_ts;
+-- There is also a PostgreSQL only index (event_contains_url_index2)
+-- which gets renamed to event_contains_url_index.
+
+-- From roommember.py
+DROP INDEX IF EXISTS room_memberships_user_room_forgotten;
+
+-- From presence.py
+DROP INDEX IF EXISTS presence_stream_state_not_offline_idx;
+
+-- From media_repository.py
+DROP INDEX IF EXISTS local_media_repository_url_idx;
+
+-- From event_push_actions.py
+DROP INDEX IF EXISTS event_push_actions_highlights_index;
+-- There's also a event_push_actions_stream_highlight_index which was previously
+-- PostgreSQL-only.
+
+-- From state.py
+DROP INDEX IF EXISTS current_state_events_member_index;
+
+-- Re-insert the background jobs to re-create the indices.
+INSERT INTO background_updates (ordering, update_name, progress_json, depends_on) VALUES
+  (7209, 'event_contains_url_index', '{}', NULL),
+  (7209, 'redactions_have_censored_ts_idx', '{}', NULL),
+  (7209, 'room_membership_forgotten_idx', '{}', NULL),
+  (7209, 'presence_stream_not_offline_index', '{}', NULL),
+  (7209, 'local_media_repository_url_idx', '{}', NULL),
+  (7209, 'event_push_actions_highlights_index', '{}', NULL),
+  (7209, 'event_push_actions_stream_highlight_index', '{}', NULL),
+  (7209, 'current_state_members_idx', '{}', NULL)
+ON CONFLICT (update_name) DO NOTHING;