A fuel cell system for power generation comprising a solid polymer type fuel cell having a solid polymer electrolyte membrane for separating an anode gas and a cathode gas, a resistor, an inverter, a switch for switching the inverter and the resister with respect to the fuel cell, the switch and the inverter, a supply conduit and discharge conduit for the anode gas and the cathode gas, and a supply vale and a discharge valve. When a molar ratio of the hydrogen contained in the anode gas to oxygen contained in the cathode gas becomes 2/1 or less at the time of the stop of the fuel cell, the supply valve for air is closed.