To make it possible to suppress the occurrence of white fog and water splashing in a fuel cell system and to discharge gas and liquid to the outside of the system while diluting fuel gas, a fuel cell system is provided wherein each of an anode off-gas passage and a cathode off-gas passage is provided with a gas-liquid separator, an exhaust passage and a drain passage are separated, a gas in the anode off-gas is mixed with a gas in the cathode off-gas and are discharged together, and a liquid in the anode off-gas is mixed with a liquid in the cathode off-gas and are discharged together. The liquid surface level of the gas-liquid separator provided in the anode off-gas passage is controlled by a controller so that the liquid surface level does not become zero when liquid is discharged. As a result, in the gas-liquid separator, it is possible to prevent the gas in the anode off-gas from flowing into the drain side. Thus, the occurrence of white fog or water splashing can be suppressed by separately providing the exhaust system and the drain system. Additionally, it is possible to dilute the fuel gas by mixing the anode exhaust gas with the cathode exhaust gas in the exhaust system.