This study deals with the thermodynamic modeling of a polymer electrolyte membrane (PEM) fuel cell power system for transportation applications. The PEM fuel cell performance model developed previously by two of the authors is incorporated into the present model. The analysis includes the operation of all the components in the system, which consists of two major modules: PEM fuel cell stack module and system module and a cooling pump. System module includes air compressor, heat exchanger, humidifier and a cooling loop. A parametric study is performed to examine the effect of varying operating conditions (e.g., temperature pressure and air stoichiometry) on the energy and exergy efficiencies of the system. Further, thermodynamic irreversibilities in each component of the system are determined. It is found that, with the increase of external load (current density), the difference between the gross stack power and net system power increases. The largest irreversibility rate occurs in the fuel cell stack. Thus, minimization of irreversibility rate in the fuel cell stack is essential to enhance the performance of the system, which in turn reduces the cost and helps in commercialization of fuel cell power system in transportation applications.