The process of adsorptive desulfurization requires sorbents to have high adsorption capacity and selectivity for thiophene in contrast to aromatics or alkanes. We investigated the adsorption of thiophene, benzene, and their mixtures in the presence of n-octane by the sodium-exchanged FAU zeolite using the grand canonical Monte Carlo simulations. The adsorption isotherms were computed and compared with available experimental data. The simulation results show that the change in the Si/Al ratio of zeolite may cause significant differences in adsorption selectivity, which was also observed by experiments. The NaX zeolite shows a higher adsorption selectivity than the NaY zeolite. The location of cations in the zeolites results in a change of pore size and creates an additional type of adsorption sit; which subsequently results in different adsorption selectivities between thiophene and benzene in model fuel.