This paper addresses the critical need to incorporate realistic models of the air supply sub-system in fuel cell system performance analysis. The paper first presents the dominant performance issues involved with the air supply operation in the fuel cell system. The report then goes on to propose a methodology for an air supply model that addresses many of the performance issues. Most importantly, a model is needed with a defined set of performance criteria and data input format, one that can accommodate multiple air supply configurations, and one that realistically and accurately simulates the air supply operation and its effect on the system power and efficiency. The paper concludes that it is possible to compare alternative air supply components under the constraint of maximizing the instantaneous net fuel cell system efficiency for a dynamic vehicle driving cycle under various ambient conditions.