To provide a fuel cell system configured to charge a battery with maintaining the independence and redundancy of a fuel cell and a battery as power sources. A fuel cell system for air vehicles, wherein the fuel cell system comprises a fuel cell, a battery, a motor and a controller; wherein the fuel cell and the battery are connected to the motor as independent power sources, and the motor includes a double three-phase winding that uses a double inverter; and wherein, when normal output is requested from the motor, the controller operates the motor by a predetermined first output from the fuel cell, and the controller charges the battery by a torque generated in the motor.