diff --git a/changelog.d/12903.bugfix b/changelog.d/12903.bugfix
new file mode 100644
index 000000000000..f26439948371
--- /dev/null
+++ b/changelog.d/12903.bugfix
@@ -0,0 +1 @@
+Fix a long-standing bug which caused the `/messages` endpoint to return an incorrect `end` attribute when there were no more events. Contributed by @Vetchu.
diff --git a/synapse/handlers/pagination.py b/synapse/handlers/pagination.py
index 6f4820c240cc..35afe6b8559e 100644
--- a/synapse/handlers/pagination.py
+++ b/synapse/handlers/pagination.py
@@ -515,14 +515,25 @@ async def get_messages(
 
             next_token = from_token.copy_and_replace(StreamKeyType.ROOM, next_key)
 
-        if events:
-            if event_filter:
-                events = await event_filter.filter(events)
+        # if no events are returned from pagination, that implies
+        # we have reached the end of the available events.
+        # In that case we do not return end, to tell the client
+        # there is no need for further queries.
+        if not events:
+            return {
+                "chunk": [],
+                "start": await from_token.to_string(self.store),
+            }
 
-            events = await filter_events_for_client(
-                self.storage, user_id, events, is_peeking=(member_event_id is None)
-            )
+        if event_filter:
+            events = await event_filter.filter(events)
+
+        events = await filter_events_for_client(
+            self.storage, user_id, events, is_peeking=(member_event_id is None)
+        )
 
+        # if after the filter applied there are no more events
+        # return immediately - but there might be more in next_token batch
         if not events:
             return {
                 "chunk": [],