Proton exchange membrane fuel cells (PEMFCs) run on pure hydrogen and oxygen (or air), producing electricity, water, and some heat. This makes PEMFC an attractive option for clean power generation. PEMFCs also operate at low temperature which makes them quick to start up and easy to handle. PEMFCs have several important limitations which must be overcome before commercial viability can be achieved. Active areas of research into making them commercially viable include reducing the cost, size and weight of fuel cells while also increasing their durability and performance. A growing and important part of this research involves the computer modeling of fuel cells. High quality computer modeling and simulation of fuel cells can help speed up the discovery of optimized fuel cell components. Computer modeling can also help improve fundamental understanding of the mechanisms and reactions that take place within the fuel cell. The work presented in this thesis describes a procedure for utilizing computer modeling to create high quality fuel cell simulations using Ansys Fluent 12.1. Methods for creating computer aided design (CAD) models of fuel cells are discussed. Detailed simulation parameters are described and emphasis is placed on establishing convergence criteria which are essential for producing consistent results. A mesh sensitivity study of the catalyst and membrane layers is presented showing the importance of adhering to strictly defined convergence criteria. A study of iteration sensitivity of the simulation at low and high current densities is performed which demonstrates the variance in the rate of convergence and the absolute difference between solution values derived at low numbers of iterations and high numbers of iterations.