This work focused on the computational fluid dynamics (CFD) modeling of H2/N2 separation in a membrane permeator module containing a supported dense Pd-based membrane that was prepared using electroless pore-plating (ELP-PP). An easy-to-implement model was developed based on a source–sink pair formulation of the species transport and continuity equations. The model also included the Darcy–Forcheimer formulation for modeling the porous stainless steel (PSS) membrane support and Sieverts’ law for computing the H2 permeation flow through the dense palladium film. Two different reactor configurations were studied, which involved varying the hydrogen flow permeation direction (in–out or out–in). A wide range of experimental data was simulated by considering the impact of the operating conditions on the H2 separation, such as the feed pressure and the H2 concentration in the inlet stream. Simulations of the membrane permeator device showed an excellent agreement between the predicted and experimental data (measured as permeate and retentate flows and H2 separation). Molar fraction profiles inside the permeator device for both configurations showed that concentration polarization near the membrane surface was not a limit for the hydrogen permeation but could be useful information for membrane reactor design, as it showed the optimal length of the reactor.