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A model of a system including a proton exchange membrane (PEM) fuel cell and its fuel processing section has been developed. The goal was to investigate the process configurations to identify the optimal operating conditions and the optimal process structure of the system by applying modeling and process integration techniques. A simulation model using commercial chemical process simulation software (BELSIM-VALI) has been developed. The model includes a steam methane reforming (SMR), a water gas shift (WGS) and a preferential oxidation (PROX) for the fuel processing feeding a proton exchange membrane cell stack (PEM) and a post-combustion unit. The energy and the material flows obtained by simulation have been used to compute the process composite curves of the system. This has been used to identify the best heat exchange opportunities and to define the optimal operating conditions of the reforming system in order to provide the best overall efficiency considering the balance of plant. By improving the energy integration of the system and by using optimisation of operating conditions, the efficiency can be raised from 35% for the reference system to up 49% in the optimized design. This is obtained both by process configuration modifications and by optimizing operating set-points. The model developed has been used for sensitivity analysis and will serve as a basis for further process design including the optimal structure determination and the thermo-economic optimisation.