A fuel cell system including a hydrogen exhaust valve provided in an outlet of a hydrogen tank, the hydrogen tank configured to supply hydrogen to a fuel cell stack, the hydrogen exhaust valve being configured to exhaust remaining hydrogen in the hydrogen tank to an outside, and a controller configured to diagnose a fault cause when a fault occurs during a flight of a flying object associated with the fuel cell stack, perform an exhaust operation on the hydrogen stored in the hydrogen tank responsive to the fault cause, and control the hydrogen exhaust valve according to the exhaust operation.