diff --git a/changelog.d/13422.bugfix b/changelog.d/13422.bugfix
new file mode 100644
index 000000000000..3a099acbe6b8
--- /dev/null
+++ b/changelog.d/13422.bugfix
@@ -0,0 +1 @@
+Fix a long-standing bug where the `update_synapse_database` script could not be run with multiple databases. Contributed by @thefinn93 @ Beeper.
\ No newline at end of file
diff --git a/synapse/_scripts/update_synapse_database.py b/synapse/_scripts/update_synapse_database.py
old mode 100755
new mode 100644
index fb1fb83f50d9..0adf94bba68f
--- a/synapse/_scripts/update_synapse_database.py
+++ b/synapse/_scripts/update_synapse_database.py
@@ -15,7 +15,6 @@
 
 import argparse
 import logging
-import sys
 from typing import cast
 
 import yaml
@@ -100,13 +99,6 @@ def main() -> None:
     # Load, process and sanity-check the config.
     hs_config = yaml.safe_load(args.database_config)
 
-    if "database" not in hs_config and "databases" not in hs_config:
-        sys.stderr.write(
-            "The configuration file must have a 'database' or 'databases' section. "
-            "See https://matrix-org.github.io/synapse/latest/usage/configuration/config_documentation.html#database"
-        )
-        sys.exit(4)
-
     config = HomeServerConfig()
     config.parse_config_dict(hs_config, "", "")