A fuel cell system enables time required for purging to be reduced without a major increase in discharge gas concentration at a time of purging. It comprises a fuel cell; a fuel gas supply path for supplying the fuel gas to an anode; an oxidizing gas supply path for supplying an oxidizing gas to a cathode; a fuel gas circulating path for returning an unreacted fuel gas to an anode inlet side; a dilution box for diluting the fuel gas by the oxidizing gas and for discharging it to outside; and a fuel gas discharge path connecting the fuel gas circulating path and a dilution box discharge gas inlet. A drain valve, a purge valve and an air discharge valve are provided, opening areas of which are different from one another. The drain valve with a smallest opening area is initially opened.