diff --git a/changelog.d/11042.bugfix b/changelog.d/11042.bugfix
new file mode 100644
index 0000000000..536c47417d
--- /dev/null
+++ b/changelog.d/11042.bugfix
@@ -0,0 +1 @@
+Work around a regression, introduced in Synapse 1.39.0, that caused `SynapseError`s raised by the experimental third-party rules module callback `check_event_allowed` to be ignored.
diff --git a/synapse/events/third_party_rules.py b/synapse/events/third_party_rules.py
index d94b1bb4d2..976d9fa446 100644
--- a/synapse/events/third_party_rules.py
+++ b/synapse/events/third_party_rules.py
@@ -217,6 +217,15 @@ class ThirdPartyEventRules:
         for callback in self._check_event_allowed_callbacks:
             try:
                 res, replacement_data = await callback(event, state_events)
+            except SynapseError as e:
+                # FIXME: Being able to throw SynapseErrors is relied upon by
+                # some modules. PR #10386 accidentally broke this ability.
+                # That said, we aren't keen on exposing this implementation detail
+                # to modules and we should one day have a proper way to do what
+                # is wanted.
+                # This module callback needs a rework so that hacks such as
+                # this one are not necessary.
+                raise e
             except Exception as e:
                 logger.warning("Failed to run module API callback %s: %s", callback, e)
                 continue