Proton exchange membrane (PEM) fuel cells have been identified as a viable emerging technology for future power generation systems in terms of both stationary and mobile applications since it offers a significant economical and environmental potential in future power production. This paper presents the development of a PEM fuel cell system using a full three-dimensional computational fluid dynamics model for the system optimization. The fuel cell investigated is a seven serpentine channel cell of 100cm2 active area. The model includes a complete set of mathematical equations for the fluid flow, multi-component species transport, electrochemistry, and the transport of protons and electrical currents throughout the PEM fuel cell. The results obtained from the parametric analyses of the cell performance at different current loads have been presented. The model results provide us detailed information on the fluid dynamics and electrochemical processes that occur in the fuel cell. This generates a clear picture on the fuel/oxidant distribution, consumption, and the current density distribution in the fuel cell. This assists us in identifying the critical parameters that influence the cell performance and sheds light onto the physical mechanisms leading to the improvement of the fuel cell system performance.