A fuel cell system includes a fuel cell stack including fuel and air electrodes, a fuel gas supply module configured to supply hydrogen and oxygen, as fuel gases, to the fuel cell stack, a fuel gas supply line including channels through which the fuel gases are supplied to the fuel cell stack, a humidification module disposed in the fuel gas supply line and configured to supply moisture to the fuel gases, and a controller configured to control the fuel gas supply line such that the fuel gases bypass the humidification module and are directly supplied to the fuel cell stack when temperature of the fuel cell stack is determined low at an initial stage of operation of the fuel cell stack, and the fuel gases pass through the humidification module and are supplied to the fuel cell stack when the temperature reaches a normal temperature.