Solid Oxide Fuel Cell (SOFC) systems achieve high electrical efficiency and can utilize many types of fuels such as methanol or biogas. These systems operate at high temperatures up to 600–1000 °C. Due to high temperatures, mechanical engineering must be combined with thermal engineering through the design work. System design for SOFC systems should take into account several functions such as mechanical support of components, thermal insulation, instrumentation, compensation for thermal expansion and heat recovery as well as conduction of gases through channels, piping or open cavities. One should note that many of these functions have strong interactions and cannot be designed without an effect on the system as a whole. When a system is designed to fulfill all the expectations, it will have a compact size, good thermal properties, small pressure losses and good overall performance together with a competitive price, long system lifetime and easy maintenance. This article aims to improve the mechanical structure of SOFC systems. In addition, our aim is to give sophisticated recommendations for a system design. To achieve this, we have used systematic concept development tools and methodologies to investigate the interactions and relative importance of system requirements and functions. Our key result from this study is that engineers must use a holistic approach when designing a high temperature system with strong interactions between system functions and components. Contrary to our former expectations, these systems could not be designed well by methods that are based on reductionism. In practice, this means that thermal engineering must be utilized from the very beginning. Thermal insulation concept should be selected during the first design steps since this has a great effect on system layout. Mechanical engineering is needed in system layout design in order to solve problems related to the thermal expansion and support of components. Combined thermal and structural analysis utilizing finite element methods can be used to develop or optimize mechanical key components and system layout. The best results can be achieved by using a holistic approach during the design process. In addition, it is beneficial to keep the system as simple and compact as possible. To achieve this, the integration of functions and components must be increased. Thus, SOFC system performance is greatly dependent on system design, not only of its components alone. Findings obtained from this study can be used by researchers designing experimental apparatuses or by companies manufacturing full scale SOFC systems.