Molecular modeling of methane permeation though silicalite membranes, including the intercrystalline region, was carried out. We focused on the effect of the intercrystalline region on sorption and diffusion properties. Molecular dynamics (MD) and grand canonical ensemble Monte Carlo (GCMC) simulations were performed to estimate the diffusion coefficient and adsorption parameters. The result of the MD calculation indicates that the intrinsic diffusivity of methane decreases by an order of magnitude due to the presence of the intercrystalline region, although the adsorption properties do not change except at higher pressure (> 2000 kPa) where the adsorption increased slightly. The estimated permeability using these parameters based on the combined method of molecular simulation and permeation theory agree well with experiments. These results indicate the importance of considering the effect of an intercrystalline region on the permeability in zeolite membranes.