A fuel cell system has a fuel cell, a gas supply device and an electronic control unit. The gas supply device supplies a scavenging gas to the fuel cell. The electronic control unit controls scavenging of the fuel cell with the scavenging gas when a request for discontinuing power generation is given to the fuel cell. A humidification control device for controlling humidification of the scavenging gas and a cooling control device for controlling cooling of the scavenging gas are provided in a passage connecting the gas supply device and the fuel cell.