Fuel cells are suitable for a power plant of a unmanned aerial vehicle (UAV) as it is not only environmentally friendly and quiet but also more efficient than an internal combustion engine. A fuel cell hybrid UAV has better performance in endurance than a fuel cell only or battery only UAV. One of the key purposes of making fuel cell hybrid UAVs is having long endurance and now maximum 26 hours of flight is possible. Because optimal design and control methods for fuel cell hybrid UAVs are absolutely needed for their long endurance we have to check the methods. The aircraft made by using application-integrated design method has less BOP mass and better performances. The optimal design and control methods are generally based on computer simulations or Hardware-In-The-Loop simulations by using dynamic models for their design and control. The Hardware-In-The-Loop simulation (HILS) is to use a hardware device like a fuel cell stack as well as a simulation program and it allows for making optimally designed applications. This paper introduce efficient methods of design, control and evaluation for the fuel cell hybrid UAVs.