In a fuel cell system, a preceding-stage fuel cell and a following-stage fuel cell are connected via a fuel flow path. The fuel cell system includes a reformer that supplies reformed gas to the preceding-stage fuel cell; an acquisition unit that acquires the amount of heat generation and the amount of heat absorption of the preceding-stage fuel cell; and a control unit that controls at least one of the amount of current of the preceding-stage fuel cell, the flow rate of air to be supplied to the reformer, and the temperature of the preceding-stage fuel cell if the amount of heat absorption acquired by the acquisition unit is larger than the amount of heat generation acquired by the acquisition unit.