The conceptual design of a bioethanol processor for fuel cell applications with heat integration was analyzed via model-based optimization formulation. Basically, the system consists of steam reforming of bioethanol and hydrogen purification process that are coupled to a proton electrolyte membrane fuel cell (PEMFC). The system was implemented within General Algebraic Modeling System (GAMS). The model simultaneously handles the problem of optimal heat integration while performing the optimization of process flowsheet. A 50 kW power generation system is presented as case study; the objective was to obtain the operative conditions for the process units that maximize the system efficiency. The operating variables of the system considered as decision variables were: system pressure, water-ethanol molar ratio and reforming temperature, input temperatures to hydrogen purification reactors, fuel cell temperature, and fuel cell hydrogen and oxygen utilizations. The results obtained predict a global efficiency of 43%, about 5% higher than the reference case. These results demonstrate the importance of simultaneous optimal heat integration for fuel cell-based processes.