A venting methodology and system for rapid shutdown of a fuel cell apparatus of the type used in a vehicle propulsion system. H.sub.2 and air flows to the fuel cell stack are slowly bypassed to the combustor upon receipt of a rapid shutdown command. The bypass occurs over a period of time (for example one to five seconds) using conveniently-sized bypass valves. Upon receipt of the rapid shutdown command, the anode inlet of the fuel cell stack is instantaneously vented to a remote vent to remove all H.sub.2 from the stack. Airflow to the cathode inlet of the fuel cell stack gradually diminishes over the bypass period, and when the airflow bypass is complete the cathode inlet is also instantaneously vented to a remote vent to eliminate pressure differentials across the stack.