The flow field plate of a proton exchange membrane fuel cell (PEMFC) functions as electron conductor and provides the pathway for oxidant and fuel to reach the membrane electrode assembly (MEA). CFD-based simulation tools can be effective in designing and optimization of flow field plates as they cab fully account for the complexity and coupling of various transport phenomena as well as the 3-D geometry. The objective of this paper is to report on the development of such a simulation platform and on its application to investigate the impact of several geometric parameters on fuel cell performance and detailed distribution of transport processes. The simulation tool is built upon a commercial computational fluid dynamics (CFD) code, CFD-ACE+, along with supporting software and script codes to automate the design workflow. A 3-D, straight channel model with material properties and model parameters validated with experimental data is used as the baseline for the present study. The workflow includes automated grid generation, model setup and job execution. Parametric study is performed for geometric parameters including (1) Channel width versus land area width (2) Channel height (3) Channel pitch and length, as well as material parameters including (4) Porosity and (5) Electrical conductivity of the gas diffusion layer (GDL). Among these parameters, it is found that predicted cell performance is most sensitive to the channel/land width ratio and to the anisotropy of the GDL property. When isotropic properties are used for the GDL, the predicted cell performance decreases with increasing channel/land width ratio. This is because the current distribution in the MEA is dictated by electrical conduction through the GDL and increasing channel width causes current to peak underneath the land area, which in turn increases ohmic losses. When the in-plane electrical conductivity is reduced, the effect of mass transfer on the current distribution becomes comparable to electron transfer and the predicted trend line of cell performance shows an optimum value as a function of the channel/land width ratio. The CFD based design tool developed in the present work has the advantage of providing more reliable prediction than methods based on reduced dimensionality or simplified transport models.