A fuel cell system comprises a fuel cell stack, a cell voltage monitor, a hydrogen tank, a hydrogen supply channel, an ejector, a hydrogen off-gas channel, a purge valve, a compressor, an air supply channel, a pressure control unit for controlling air pressure, a pilot pressure input channel branching off from the air supply channel and inputting the air pressure to the ejector as pilot pressure, and a control unit for controlling the purge valve and the pressure control unit. The ejector includes a pressure control mechanism which increases the ejector's secondary-side pressure by increasing the area of the nozzle's ejecting hole when the pilot pressure input from the pilot pressure input channel rises. When electricity generation status of the fuel cell stack is judged to be poor, the control unit opens the purge valve after raising the air pressure and the pilot pressure by using the pressure control unit.