In the context of stationary power generation, fuel cell-based systems are being foreseen as a valuable alternative to thermodynamic cycle-based power plants, especially in small scale applications. As the technology is not yet established, many aspects of fuel cell devel- opment are currently investigated worldwide. Part of the research focuses on integrating the fuel cell in a system that is both efficient and economically attractive. To address this problem, we present in this paper a thermo-economic optimization method that systematically generates the most attractive configurations of an 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. A solid oxide fuel cell (SOFC) system of 50 kW integrat- ing a planar SOFC is modeled and optimized leading to designs with efficiencies ranging from 34% to 44%. The multi-objective optimi- zation strategy identifies interesting system configurations and their performance for the developed SOFC system model. The methods proves to be an attractive tool to be used both as an advanced analysis tool and as support to decision makers when designing new systems.