The fuel cell system of the present invention includes: (A) a fuel cell stack including at least one unit fuel cell including a cathode, an anode, and a polymer electrolyte membrane interposed therebetween; (B) a detecting device for detecting lack of humidification in the fuel cell stack; (C) a water supplying device for supplying moisture to the fuel cell stack when lack of humidification is detected by the detecting device; (D) a heating device for heating the supplied moisture; and (E) a cooling device for cooling the supplied moisture. In the fuel cell system of the present invention, the fuel cell stack is humidified by repeating heating and cooling of the supplied moisture by the heating device and the cooling device, respectively.