Biogas reforming in membrane reactors has been considered an alternative for hydrogen-rich stream production. Since this technology is not yet applied in industry, the performance of this process can only be evaluated by theoretical simulations. In this work, H2 production employing biogas as feedstock was simulated by Computational Fluid Dynamics in Pd membrane reactors, considering a two-dimensional and non-isothermal model on laboratory and industrial (20 times greater) scales. The most relevant operating parameters were external temperature and residence time (or inlet velocities). An optimal temperature range was proposed (823–948 K) to achieve a balance between reaction performance and H2 permeation rate. Significant thermal gradients were observed on the industrial scale, showing that non-isothermal modeling is crucial for designing a membrane reactor with larger dimensions. The better reaction performance was obtained at lower velocities (<0.046 m s−1), which is also an important information for the optimization and design of the membrane modules.