This paper presents a two-dimensional model to describe the gas flow in an integrated reactor, developed at the CNR-ITAE Institute, and aimed to design a hydrogen generator, named HYGen II, to integrate with polymer electrolyte fuel cells (PEFCs) for residential applications. The model is able to simulate velocity profiles in order to investigate the reactor geometrical key parameters. The unit can convert light hydrocarbons (methane, propane, LPG, butane) into a hydrogen rich mixture. The processing unit consists of an innovative integrated dual bed reactor, filled with pellet catalysts: a proprietary autothermal reforming (ATR) and a commercial intermediate temperature water gas shift (ITWS). For the last clean-up step, a single-stage preferential oxidation (PROX) process has been adopted. Moreover, an automation system to monitor operating conditions and control plant equipment has been designed.