Fuel cell systems integrate the fuel cell technology with fuel processing and post processing. A thermo-economic optimization method has been developed to systematically generate the most attractive configurations of the integrated system. In the developed methodology, the energy flows are computed using conventional process simulation software. The system is integrated using the pinch based methods that rely on optimization techniques. This defines the minimum of energy required and sets the basis to design the ideal heat exchanger network. A thermo-economic method is then used to compute the integrated system performances, sizes and costs. This allows performing the optimization of the system with regard to two objectives: minimize the specific cost and maximize the efficiency. The multi-objective optimization strategy identifies interesting system configurations and their performance. This method will be used as a support for decision makers when designing a new system. In this paper, the methodology is applied to study the integration of a Solid Oxide Fuel Cell system.