A method of operating a fuel cell system which is controlled by an electronic device includes: transmitting a bit stream including a bit string which indicates identification information of the fuel cell system and a bit string which indicates status information of the fuel cell system to the electronic device through a serial communication line; receiving a bit stream including a bit string which indicates control information of the fuel cell system from the electronic device through the serial communication line; obtaining the control information of the fuel cell system from the received bit stream; and controlling power production of a fuel cell by controlling operations of peripheral devices of the fuel cell system based on the obtained control information of the fuel cell system.