Catalyst layer modeling can be a useful tool for fuel cell design. By comparing numerical results to experimental results, numerical models can provide a better understanding of the physical processes occurring within the fuel cell catalyst layer. This can lead to design optimization and cost reduction. The purpose of this research was to compare, for the first time, a direct numerical simulation (DNS) model for the cathode catalyst layer of a PEM fuel cell to a newly developed experimental technique that measures the ionic potential through the length of the catalyst layer. A new design for a microstructured electrode scaffold (MES) is proposed and implemented. It was found that there is a 25%-27% difference between the model and the experimental measurements. Case studies were also performed with the DNS to compare the effects of different operating conditions, specifically temperature and relative humidity, and different reconstructed microstructures. Suggested operating parameters are proposed for the best comparison between numerical and experimental results. Recommendations for microstructure reconstruction, MES construction and design, and potential measurement techniques are also given. / Master of Science