A fuel cell system comprising: a fuel cell (2, 23) that generates power by using fuel; an exhaust gas path on which an exhaust gas flows; a water circulation path on which cooling water for cooling heat generated from the fuel cell (2, 23) circulates; a first heat exchanging apparatus that is provided on the exhaust gas path and the water circulation path and performs heat exchange between the exhaust gas and the cooling water; a tank which is provided for collecting condensed water generated by cooling the exhaust gas in the first heat exchanging apparatus; a radiator that is provided on the water circulation path and dissipates heat of the cooling water; a circulation pump that is provided on the water circulation path and causes the cooling water to be circulated; and a control apparatus which is configured to operate to switch between a first operation mode and a second operation mode, the first operation mode being a mode in which the cooling water after passing through the radiator is controlled to have a first predetermined temperature, and the second operation mode being a mode in which the cooling water after passing through the radiator is controlled to have a second predetermined temperature which is higher than the first predetermined temperature, by adjusting an amount of dissipated heat of the cooling water in the radiator, the first predetermined temperature is a temperature at which collecting water of an amount required for an operation of the fuel cell system by the tank is allowed, and the second predetermined temperature is a temperature at which a mold in the cooling water on the water circulation path and water collected by the tank dies. a fuel cell (2, 23) that generates power by using fuel; an exhaust gas path on which an exhaust gas flows; a water circulation path on which cooling water for cooling heat generated from the fuel cell (2, 23) circulates; a first heat exchanging apparatus that is provided on the exhaust gas path and the water circulation path and performs heat exchange between the exhaust gas and the cooling water; a tank which is provided for collecting condensed water generated by cooling the exhaust gas in the first heat exchanging apparatus; a radiator that is provided on the water circulation path and dissipates heat of the cooling water; a circulation pump that is provided on the water circulation path and causes the cooling water to be circulated; and a control apparatus which is configured to operate to switch between a first operation mode and a second operation mode, the first operation mode being a mode in which the cooling water after passing through the radiator is controlled to have a first predetermined temperature, and the second operation mode being a mode in which the cooling water after passing through the radiator is controlled to have a second predetermined temperature which is higher than the first predetermined temperature, by adjusting an amount of dissipated heat of the cooling water in the radiator, the first predetermined temperature is a temperature at which collecting water of an amount required for an operation of the fuel cell system by the tank is allowed, and the second predetermined temperature is a temperature at which a mold in the cooling water on the water circulation path and water collected by the tank dies.