A fuel cell system includes: a fuel cell; a temperature acquisition unit that acquires a temperature at a specific position in a vehicle equipped with the fuel cell system; a purge unit that purges the fuel cell when an operation of the fuel cell is stopped; and a control unit that acquires the temperature at the specific position from the temperature acquisition unit at least once from when the fuel cell system is stopped until the fuel cell system is started again, and uses the temperature at the specific position to determine whether purging at a stop by the purge unit is necessary when the fuel cell system is stopped next.