A fuel cell system including a fuel cell, and a converter which is connected between the fuel cell and a high voltage system and which sets an output ceiling voltage of the fuel cell, the fuel cell system comprising fuel gas supply stopping means for stopping the supply of fuel gas to the fuel cell in an intermittent operation mode, remaining fuel gas amount determination means for determining whether fuel gas in at least an amount capable of generating power remains in the fuel cell, converter driving means for driving the converter so that, when it is determined that fuel gas in at least the amount capable of generating power remains in the fuel cell, the output ceiling voltage of the fuel cell becomes a first voltage capable of preventing deterioration of the fuel cell, and converter stopping means for stopping the converter when it is determined that fuel gas in at least the amount capable of generating power does not remain in the fuel cell.