A control method of a fuel cell system includes generating electricity in a fuel cell through reaction of an oxidant gas and a fuel gas so as to output a fuel cell voltage. An electric storage device voltage is outputted from an electric storage device. The electric storage device voltage serves as a primary side voltage. A motor driving voltage serves as a secondary side voltage and is to be applied to a motor driving device to drive a motor. The secondary side voltage is applied to an air pump driving device to drive an air pump so as to supply the oxidant gas to the fuel cell. A required air pump voltage to apply to the air pump driving device is set in accordance with a target generated electric power of the fuel cell. The secondary side voltage is set so as to satisfy the required air pump voltage.