A fuel cell system is equipped with a plurality of subsystems. Each of the plurality of the subsystems is equipped with a fuel cell stack, a temperature sensor, a scavenging device, and a control unit. The control unit of that one of the subsystems having the fuel cell stack whose temperature is specified as being the lowest among the plurality of the subsystems when the fuel cell system is stopped from operating performs scavenging control including a determination on the carrying out of scavenging in the subsystem and the issuance of a command to carry out scavenging to all the subsystems in accordance with the determination.