The invention provides a fuel cell system which can reduce the power consumption after emergency stop. At an ordinary stop time of a fuel cell system, a controller of the fuel cell system completes an ordinary stop process that includes at least one of a water drainage process that discharges water from at least one of the fuel gas flow path and the oxidizing gas flow path and a cathode sealing process that seals the oxidizing gas flow path, and subsequently stops the fuel cell system. When the fuel cell system satisfies a predetermined emergency stop condition, the controller does not perform at least part of the ordinary stop process but performs an emergency stop process that sets the fuel cell system to be restarted after elapse of a first time period since a stop of the fuel cell system and subsequently stops the fuel cell system. The controller restarts the fuel cell system after elapse of the first time period since stop of the fuel cell system and performs a restart process that performs the ordinary stop process.