To provide a fuel-efficient fuel cell system configured to eliminate flooding in a fuel-based gas flow path, etc. The fuel cell system is a fuel cell system comprising a first fuel cell stack, a second fuel cell stack, a fuel gas supplier, a first supply flow path, a first circulation flow path, a second supply flow path, a second circulation flow path, a first bypass flow path which includes a first on-off valve, a second bypass flow path which includes a second on-off valve, a temperature detector, a current detector, a voltage detector and a controller.