diff --git a/changelog.d/4214.misc b/changelog.d/4214.misc
new file mode 100644
index 0000000000..b2f62060e3
--- /dev/null
+++ b/changelog.d/4214.misc
@@ -0,0 +1 @@
+Ignore __pycache__ directories in the database schema folder
diff --git a/synapse/storage/prepare_database.py b/synapse/storage/prepare_database.py
index bd740e1e45..d5d2f89a77 100644
--- a/synapse/storage/prepare_database.py
+++ b/synapse/storage/prepare_database.py
@@ -257,7 +257,7 @@ def _upgrade_existing_database(cur, current_version, applied_delta_files,
                 module.run_create(cur, database_engine)
                 if not is_empty:
                     module.run_upgrade(cur, database_engine, config=config)
-            elif ext == ".pyc":
+            elif ext == ".pyc" or file_name == "__pycache__":
                 # Sometimes .pyc files turn up anyway even though we've
                 # disabled their generation; e.g. from distribution package
                 # installers. Silently skip it