In a method of operating a fuel cell system, a stable-period voltage difference is calculated in a state where output power of the fuel cell stack is stable. Thereafter, a voltage difference is calculated during power generation. Then, it is determined whether or not the change amount of the voltage difference with respect to the stable-period voltage difference has exceeded a predetermined threshold value. When it is determined that the change amount has exceeded the predetermined threshold value, electric power is generated with the supply amount of the anode gas to the fuel cell stack being increased.