A fuel cell system operating method in which a temperature of a fuel cell power generator is measured when the fuel cell power generator stops generating power, and it is determined whether the temperature is within a predetermined temperature range, and a reverse current is supplied to the fuel cell power generator upon restart if the temperature was determined to be outside of the predetermined range so as to increase the efficiency of the system after restarting the fuel cell power generator after being exposed to extreme conditions. Subsequently, the reverse current supply to the fuel cell power generator stops and electric energy is generated through an electrochemical reaction between hydrogen and oxygen in the fuel cell power generator.