A fuel cell system calculates amount of fluid discharged from a fuel gas circulation path with water and fuel gas in accordance with an ordinary process map if inside an anode is not scavenged when a fuel cell stops electrochemical reaction; measures amount of water remaining in a fuel gas circulation path in accordance with cumulative electricity output, temperature, or elapsed time after starting the electrochemical reaction if the inside the anode is scavenged previously; and determines whether the inside the fuel gas circulation path is in dry condition or humid condition. The fuel cell system calculates amount of fluid discharged from the fuel gas circulation path with water or the fuel gas in accordance with a map predetermined for the dry condition if the fuel cell system determines that the inside the fuel gas circulation path is in the dry condition. The fuel cell system calculates the amount of the fluid to be discharged with the water or the fuel gas in accordance with the ordinary map if the fuel cell system determines that the inside the fuel gas circulation path is in the humid condition. Accordingly, wasteful discharge of fuel gas can be prevented in a purging operation after starting up the fuel cell system.