Saturated and unsaturated permeabilities are influenced by the microscopic pore structure of granular porous media. We developed pore flow simulations for grains generated by discrete-element modeling to evaluate the effect of grain shape (aspect ratio) on permeability and other macroscopic properties related to fluid flow. A series of sensitivity analyses was performed for methodological variables, such as the mesh resolution and the size of the simulated soil volume. The simulation results were found to be consistent with the conventional Darcy’s law. Consistent with the Kozeny–Carman equation, the results of simulations for grains with various aspect ratios confirmed that permeability depends on the void ratio. We also found that the grain aspect ratio affected the void ratio and the surface area of packed grains. Consequently, the aspect ratio indirectly affected the permeability.