To provide a fuel cell system configured to prevent the freezing of the gas and water discharge valve of the fuel gas system even at high altitude. A fuel cell system for air vehicles, wherein the fuel cell system comprises: a fuel cell, a fuel gas system for supplying fuel gas to the fuel cell, a cooling system for controlling a temperature of the fuel cell, an altitude sensor, a temperature sensor, and a controller, and wherein, when the controller detects an altitude increase measured by the altitude sensor, and when a temperature of the gas and water discharge valve measured by the temperature sensor is less than a predetermined temperature, the controller increases a temperature of the refrigerant by controlling the three-way valve to circulate the refrigerant in the heating flow path and operating the circulation pump and the water heater to heat the refrigerant.