Polymer electrolyte membrane (PEM) fuel cell stacks are constructed by stacking several to hundreds of unit cells depending on their power outputs required. Fuel and oxidant are distributed to each cell of a stack through so-called manifolds during its operation. In designing a stack, if the manifold sizes are too small, the fuel and oxidant would be maldistributed among the cells. On the contrary, the volume of the stack would be too large if the manifolds are oversized. In this study, we present a three-dimensional computational fluid dynamics (CFD) model with a geometrically simplified flow-field to optimize the size of the manifolds of a stack. The flow-field of the stack was simplified as a straight channel filled with porous media to reduce the number of computational meshes required for CFD simulations. Using the CFD model, we determined the size of the oxidant manifold of a 30 kW-class PEM fuel cell stack that comprises 99 cells. The stack with the optimal manifold size showed a quite uniform distribution of the cell voltages across the entire cells.