A fuel cell system comprises: a gas-liquid separator separating exhaust gas of a fuel cell stack into a liquid component and a gas component and storing liquid water of the liquid component; a circulation pipe; a drain pipe discharging the liquid water; and a drain valve opening and closing the drain pipe. In an end scavenging process that is executed when operation of the fuel cell system is finished, the control unit opens the drain valve when a valve opening condition for the drain valve is satisfied. The valve opening condition is set such that an amount of the liquid water stored in the gas-liquid separator at the time the drain valve is opened in the end scavenging process is larger than an amount of the liquid water stored in the gas-liquid separator at the time the drain valve is opened during normal operation of the fuel cell system.