The stringent emission regulation and future shortage of fossil fuel motivate the research of alternative powertrain. In this study, a system of proton exchange membrane fuel cell has been modeled to analyze the performance of the fuel cell system for automotive application. The model is composed of the fuel cell stack, air compressor, humidifier, and intercooler, and hydrogen supply which are implemented by using the Matlab/Simulink(R). Fuel cell stack model is empirical model but the water transport model is included so that the system performance can be predicted over various humidity conditions. On the other hand, the model of air compressor is composed of motor, static air compressor, and some manifolds so that the motor dynamics and manifold dynamics can be investigated. Since the model is concentrated on the strategic operation of compressor to reduce the power consumption, other balance of components (BOP) are modeled to be static components. Since the air compressor model is empirical model which is based on curve fitting of experiments, the stack model is validated with the commercial software and the experiments. The dynamics of air compressor is investigated over unit change of system load. The results shows that the power consumption of air compressor is about 12% to 25% of stack gross power and dynamic response should be reduced to optimize the system operation.