diff --git a/src/ctapipe/core/tool.py b/src/ctapipe/core/tool.py
index 5e42e4ad4b5..6325c909b53 100644
--- a/src/ctapipe/core/tool.py
+++ b/src/ctapipe/core/tool.py
@@ -460,6 +460,8 @@ def run(self, argv=None, raises=False):
                     # Finish normally
                     Provenance().finish_activity(activity_name=self.name)
                 else:
+                    if raises:
+                        raise
                     # Finish with error
                     self.log.critical(
                         "Caught SystemExit with exit code %s", exit_status