Summary This work investigates the operation of a small-scale shell-and-tube-shaped module for separating hydrogen from high-pressure post-shift syngas that would be produced in integrated gasification combined cycle plants. The separation occurs via permeation through palladium membranes that form the wall of the tubes. The main objective is to examine the effect of four design variables on the permeation performance. These variables are (i) flow rate, (ii) baffle spacing, (iii) inserting stinger tubes inside the permeate tubes, and (iv) switching the permeate stream from the tubes to the shell. The problem is treated by using three-dimensional multi-species computational fluid dynamic models, incorporating the Sievert's law for the permeation action. Quantitative assessment of the permeation and the incurred pressure drop was done by monitoring key integral parameters, such as two-point efficiency, area-based efficiency, and hydrogen recovery. The considered variables allow a wide spectrum of operation modes. This work thus gives the interested reader a generic guideline about the module design suitable for their specific aims. Copyright © 2016 John Wiley & Sons, Ltd.