A fuel cell system includes a controller configured to control opening and closing of a drain valve and opening and closing of an exhaust valve. The controller is configured to, when an amount of water stored in a gas-liquid separator is larger than or equal to a predetermined value, open the drain valve to drain, via the drain valve, the water stored in the gas-liquid separator. The controller is configured to, when a concentration of impurities contained in circulating gas is higher than or equal to a predetermined value, open the exhaust valve to release, via the exhaust valve, the circulating gas circulating in the circulating path.