A fuel cell system comprising: an anode gas flow path supplied with an anode gas; a cathode gas flow path supplied with a cathode gas; a fuel cell generating electricity by the anode gas being supplied to the anode gas flow path and the cathode gas being supplied to the cathode gas flow path; an anode gas supplying unit supplying the anode gas to the anode gas flow path; a blowdown valve ejecting fluid from inside the anode gas flow path towards an exterior; and a control unit which controls the anode gas supplying unit and the blowdown valve, supplies the anode gas from the anode gas supplying unit to the anode gas flow path, and performs a periodic fluid substitution by opening the blowdown valve periodically, wherein the control unit comprises a low temperature condition determination unit.