A fuel cell system comprises a fuel cell, a reactant gas supply device, and a capacitor which supplies a power to various devices when the fuel cell is in a temporary power generation stop state. The fuel cell system drives the reactant gas supply device based on a predetermined current instruction value to supply a reactant gas to the fuel cell, thereby generating the power. Such a fuel cell system comprises a control device which judges whether or not the current instruction value is below a water balance zero current value when the water content of the fuel cell is below a predetermined threshold and the stored electric charge of the capacitor is a predetermined threshold or more. If affirmative judgment is obtained, the control device switches the power generation state of the fuel cell to the temporary power generation stop state.