A fuel cell system is provided that includes a fuel cell stack and an air compressor in communication with a cathode inlet, a hydrogen source in communication with an anode inlet, and a start-up battery adapted to power the air compressor. The start-up battery is at least one of a low-voltage battery and a high-voltage battery. A pressure sensor is in communication with the air compressor and adapted to measure a compressor outlet pressure. A power conversion module is in electrical communication with the start-up battery and the air compressor. A controller is in communication with the power conversion module and adapted to set an air compressor speed based on an available electrical energy. A closed-loop method of operating the fuel cell system at start-up is also provided, wherein an anode purge is scheduled based on an air flow rate calculated from the compressor outlet pressure and the actual speed.