A fuel cell system includes a fuel cell, a heater provided in the fuel cell, a load such as a peripheral component of the fuel cell, a capacitor, and a switch. Power generation of the fuel cell is carried out continuously for supplying electric energy to the load, and charging the capacitor. When charging of the capacitor is completed, the switch is operated such that electric energy discharged from the capacitor is supplied to the heater for warming up the fuel cell by the heater.