This dissertation progressively addresses research problems related to the trajectory optimization for fuel cell powered UAVs, from propulsion system model development, to optimal trajectory analyses and optimal trajectory applications. A dynamic model of a fuel cell powered UAV propulsion system is derived by combining a fuel cell system dynamic model, an electric motor dynamic model, and a propeller performance model. The influence of the fuel cell system dynamics on the optimal trajectories of a fuel cell powered UAV is investigated in two phases. In the first phase, the optimal trajectories of a fuel cell powered configuration and that of a conventional gas powered configuration are compared for point-to-point trajectory optimization problems with different performance index functions. In the second phase, the influence of the fuel cell system parameters on the optimal fuel consumption cost of the minimum fuel point-to-point optimal trajectories is investigated. This dissertation also presents two applications for the minimum fuel point-to-point optimal trajectories of a fuel cell powered UAV: three-dimensional minimum fuel route planning and path generation, and fuel cell system size optimization with respect to a UAV mission.