A numerical study is conducted to compare the current most popular flow field configurations, porous, biporous, porous with baffles, Toyota 3D fine-mesh, and traditional rectangular flow field. Operation at high current densities is considered to elucidate the effect of the flow field designs on the overall heat transfer and liquid water removal. A comprehensive 3D, multiphase, nonisothermal computational fluid dynamics model is developed based on up-to-date heat and mass transfer sub-models, incorporating the complete formulation of the Forchheimer inertial effect and the permeability ratio of the biporous layers. The porous and baffled flow field improves the cell performance by minimizing mass transport losses, enhancing the water removal from the diffusion layers. The baffled flow field is chosen for optimization owing to the simple design and low manufacturing cost. A total of 49 configurations were mutually compared in the design of experiments to show the quantitative effect of each parameter on the performance of the baffled flow field. The results elucidate the significant influence of small geometry modifications on the overall heat and mass transfer. The results of different cases have shown that water saturation can be decreased by up to 33.59% and maximal temperature by 7.91 °C when compared to the reference case which is already characterized by very high performance. The most influencing geometry parameters of the baffles on the cell performance are revealed. The best case of the 49 studied cases is further optimized by introducing a linear scaling factor. Additional geometry modifications demonstrate that the gain in performance can be increased, but at a cost of higher pressure drop and increased design complexity. The conclusions of this work aids in the development of compact and high-performance proton exchange membrane fuel cell stacks.