To investigate the influence of ‘single-file’ diffusion on nonequilibrium transport phenomena inside zeolite nanopores, we calculated permeate velocities of guest species in AFI-type AlPO₄-5 and MFI-type silicalite membranes, using a grand canonical ensemble molecular dynamics (GCMD) simulation. We chose as examples He/CH₄ and CH₄/SF₆ mixtures through AlPO₄-5, and CH₄/CF₄ mixtures through silicalite. In AlPO₄-5 systems, He permeates much faster than CH₄ in an He/CH₄ mixture, whereas CH₄ moves at nearly the same speed as SF₆ in the CH₄/SF₆ mixture. In CH₄/CF₄ mixtures in silicalite, the permeate velocity of each component becomes close to each other, compared with that of pure gas. These results suggest that ‘single-file’ permeation occurs where one guest species cannot overtake the other inside nanopores under a concentration gradient, especially if at least one component has a molecular diameter similar to the host pore size. Moreover, the calculated separation factor for CH₄/CF₄ mixtures through silicalite showed a strong correlation with the permeate velocities of the guest species, suggesting the influence of ‘single-file’ permeation on the absolute values of the separation factor. Particularly, it is concluded that the decrease in CH₄ permeate velocities directly leads to the decrease in the separation factors, compared with ideal separation factors. Finally, using these data from GCMD simulations and other molecular simulation techniques, we propose a methodology to predict transport diffusivities in binary mixtures. In this paper, the transport diffusivities of CH₄/CF₄ mixtures in silicalite were calculated based on Maxwell–Stefan (MS) theory. Further efforts to achieve the systematic estimation of these transport diffusivities will lead to the prediction of multicomponent separation factors using only single-component data.