diff --git a/changelog.d/9537.bugfix b/changelog.d/9537.bugfix
new file mode 100644
index 0000000000..033ab1c939
--- /dev/null
+++ b/changelog.d/9537.bugfix
@@ -0,0 +1 @@
+Fix rare edge case that caused a background update to fail if the server had rejected an event that had duplicate auth events.
diff --git a/synapse/storage/databases/main/events_bg_updates.py b/synapse/storage/databases/main/events_bg_updates.py
index c1626ccf28..cb6b1f8a0c 100644
--- a/synapse/storage/databases/main/events_bg_updates.py
+++ b/synapse/storage/databases/main/events_bg_updates.py
@@ -696,7 +696,9 @@ class EventsBackgroundUpdatesStore(SQLBaseStore):
                 )
 
             if not has_event_auth:
-                for auth_id in event.auth_event_ids():
+                # Old, dodgy, events may have duplicate auth events, which we
+                # need to deduplicate as we have a unique constraint.
+                for auth_id in set(event.auth_event_ids()):
                     auth_events.append(
                         {
                             "room_id": event.room_id,