A fuel cell system installed in a vehicle, the system comprising: a fuel cell, a secondary cell, a system temperature acquirer for acquiring a temperature of an inside of the fuel cell system, and a controller, wherein, when the system temperature is a predetermined first temperature or less, the controller charges the secondary cell until a state-of-charge value of the secondary cell reaches a predetermined first threshold value, and the controller carries out a first pattern purge on the fuel cell, and wherein, when the system temperature exceeds the predetermined first temperature, the controller charges the secondary cell until the state-of-charge value of the secondary cell reaches a predetermined second threshold value that is larger than the predetermined first threshold value, and the controller carries out a second pattern purge having a shorter purge time than the first pattern purge on the fuel cell.