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In this paper, the capability of the Computational Fluid Dynamics (CFD) approach is evaluated to reliably predict the fluid dynamic and the separation performance of Pd membranes modules for gas mixture separation. In this approach, the flow fields of the pressure and velocity for the gas mixture and the species concentration distribution in the selected three-dimensional domains are obtained by simultaneous and numerical solution of continuity, momentum, and species transport (especially, gas-through-gas diffusion term that derived from the Stefan–Maxwell formulation) equations. Therefore, the calculation of the hydrogen permeation depends on the local determination of the mass transfer resistance caused by the gas phase and membrane, which is modeled as a permeable surface of known characteristics. The applicability of the model to properly predict the separation process under a wide range of pressure, feed flow rate, temperature, and gas mixtures composition is assessed through a strict comparison with experimental data. Moreover, in this work, the influence of inhibitor species on the module performance is discussed, which is obtained by implementing the CFD model. The results of the simulation showed that increasing the pressure on the feed side increases the molar fraction of hydrogen gas, the feed inlet flow on the shell side, and the hydrogen permeation through the membrane in the tube side. Comparison of simulation results with laboratory data showed good agreement. The model was obtained with an error of less than 3% at 450K and below 6% for 475K and 500K.