A fuel cell system comprising a fuel cell, a means for supplying cooling water to the fuel cell, a temperature sensor for detecting the cooling water outlet temperature and the cooling water inlet temperature, and a means for regulating the temperature of the fuel cell by controlling the flow rate of refrigerant based on the cooling water outlet temperature. The fuel cell system is further provided with a means for judging whether there is an abnormality with the temperature sensor or not, and a refrigerant temperature estimation means for estimating the cooling water outlet temperature basedon physical information about the operating state of the fuel cell when there is an abnormality with the temperature sensor as a result of judgment.