There is provided a fuel cell system which is efficient and does not cause reduction in output even when operation and stopping of a fuel cell are repeated for a long period of time. The fuel cell system is provided with a fuel cell stack including a fuel chamber for supplying a hydrogen gas to a hydrogen electrode and an oxygen chamber for supplying air to an oxygen electrode. The system is provided with gas supply ports for supplying the hydrogen gas into the fuel chamber, gas discharge ports for discharging the hydrogen gas from the fuel chamber, a hydrogen suction pump and the like for sucking the hydrogen gas from the gas discharge ports, a hydrogen circulation pipe and the like for interconnecting the gas discharge ports and the gas supply ports through the hydrogen suction pump and the like, and a first hydrogen discharge pipe and the like for interconnecting the gas discharge ports and an outside gas release port through the hydrogen suction pump and the like.