Unmanned aerial vehicles (UAVs) have been applied to not only military missions like surveillance and reconnaissance but also commercial missions like meteorological observation, aerial photograph, communication relay, internet network build and disaster observation. Fuel cells make UAVs eco-friendly by using hydrogen. Proton exchange membrane fuel cells (PEMFCs) show low operation temperature, high efficiency, low noise and high energy density and those characterisitcs are well fitted with UAVs. Thus Fuel cell based UAVs have been actively developed in the world. Recently, fuel cell UAVs have started to develope for high altitude UAVs because target altitude of UAVs is expanded upto stratosphere altitude. Long endurance of UAVs is essential to improve effects of the missions. Improvement of UAV endurance time could be fulfilled by developing a hydrogen fuel storage system with high energy density and reducing the weight of UAVs. In this paper, research trend and analysis of fuel cell UAVs are introduced in terms of their altitude and endurance time and then the prospect of fuel cell UAVs are shown.