A fuel cell system is provided with a fuel cell body, a hydrogen supply system supplying hydrogen containing gas to the fuel cell body, an oxygen supply system supplying oxygen containing gas to the fuel cell body, a cooling system adjusting the temperature of the fuel cell body, a water circulation system supplying water to humidify the fuel cell body and collecting water discharged from the fuel cell body, a generated heat amount calculating section calculating a generated heat amount of the fuel cell body, a cooling performance calculating section calculating a cooling performance of the cooling system, a temperature calculating section calculating a fuel cell temperature of the fuel cell body on the basis of the generated heat amount and the cooling performance, a collected water amount calculating section calculating an amount of water collected from the water circulation system on the basis of the fuel cell temperature, and a collected water amount controlling section controlling the amount of collected water discharged from the fuel cell body on the basis of the amount of collected water.