The temporal stability and spatial homogeneity of current density are key factors in Polymer Electrolyte Fuel Cell (PEFC) performance and durability. Temporal and spatial variations of relative humidity, fuel concentration, and water droplets in the channels are the principal causes of non-homogeneous current density. A dynamic pseudo-3D model was previously proposed by the authors and has been extended and improved to perform the long-term and intensive simulations of PEFC with low computational cost, which allows to study of the performances homogeneity with different experimental configurations and flow field topologies. The model considers important phenomena in the homogeneity analysis, such as gases and liquid water movement in diffusion layers and flow field, electrochemical reactions, and others. Model validation has been performed using experimental data obtained from a 25 cm2 cell with a single serpentine, which has allowed studying the model transient response and spatial representation. The simulations have been used to study the homogeneity and stability of 36 setups of PEFC, varying the rib/channel width ratio, the stoichiometric ratio, and the number of parallel serpentine channels. The results show the importance of a properly flow field design to control gas flow, remove the channels’ liquid water, and keep a homogeneous feeding. The study evaluated a set of channel configurations that show the improved temporal voltage stability and current density spatial homogeneity. The results show the impact of channel gas speed and ratio channel/rib width in liquid droplets removal and the proper fuel spatial distribution; and how configurations with a lesser number of channels in serpentine design require a lower stoichiometric ratio to perform better temporal and spatial uniformity. In the case of the cell configurations simulated, the optimum design was achieved using between 5 and 7 parallel serpentine channels and a channel/rib ratio 3/5.