This paper describes a Proton Exchange Membrane (PEM) fuel cell system model for automotive applications that includes an air compressor, cooling system, and other auxiliaries. The fuel cell system model has been integrated into a vehicle performance simulator that determines fuel economy and allows consideration of control strategies. Significant fuel cell system efficiency improvements may be possible through control of the air compressor and other auxiliaries. Fuel cell system efficiency results are presented for two limiting air compressor cases: ideal control and no control. Extension of the present analysis to hybrid configurations consisting of a fuel cell system and battery is currently under study.