There is provided a fuel cell system capable of warming up a fuel cell while inhibiting generation of a rush current. A control device switches the connection/disconnection between a fuel cell and a short circuit by a shorting relay. The control device spends, before switching the shorting relay from disconnection to connection during starting at a low temperature, an oxidizing gas remaining in the cathode of the fuel cell by driving auxiliary devices to generate an oxidizing gas-deficient state. Then, the control device switches FC relays from ON to OFF and the shorting relay from OFF to ON to thereby complete the preparation for supplying a short-circuit current.