New power generation systems need to be clean, highly reliable, highly efficient, and competitively priced. In addition, they should possess low maintenance requirements as well as low noise levels. It is believed that fuel cell power systems can meet all these criteria in the future. For that purpose, designing a fuel cell system, including its structure and its operation, plays a crucial role. Fuel cell system designs range from very simple to very complex depending on the application and the desired system efficiency. A fuel cell system can be highly efficient with a good integration between the fuel cell stack and other plant components. However, a more complex fuel cell stack with a more complex fuel cell plant subsystem may be more efficient. Therefore, the design of the fuel cell plant with electrical subsystems and high electrical efficiency over 40% seems to be endless. Optimization strategies for the fuel cell systems, including the decision variables, objective analyses, constraints, methods and tools, have extensively attracted attention in line with the growing fuel cell applications. The objective of this chapter is to discuss the solid oxide fuel cell system design and optimization to provide better insight for future work and areas of improvement.