Due to their high energy density, proton exchange membrane (PEM) fuel cell systems are becoming increasingly attractive as the primary powerplant for low-power, long-endurance aircraft applications. Although PEM fuel cell technology has been applied for automotive and stationary use, limited design and experimental work has been performed and documented for actual aircraft applications. In order to better understand the design and performance tradeoffs for PEM fuel cell powered aircraft, a high-level conceptual design study of small-scale long-endurance aircraft is performed. This study builds upon design lessons learned through the development and flight testing of a PEM-powered demonstrator aircraft designed and built by the Georgia Institute of Technology. The study focuses on identifying and exploring the concept design space appropriate for small unmanned air vehicles with ranges of up to 5000 km flying at low altitudes with endurances of up to 64 hours. A Quality Function Deployment is used in conjunction with a Matrix of Alternatives to define multiple competing aircraft configurations based on current advanced technologies in PEM fuel cells, hydrogen storage, electric propulsion, aircraft design, and structural materials. A baseline propulsion system consisting of a liquid cooled PEM fuel cell with compressed hydrogen storage powering multiple electric tractor propeller motors was chosen. The corresponding baseline aerodynamic configuration consisted of a high-aspect ratio tapered wing with multiple tractor propellers. Eleven design variables governing the powerplant, propulsion, and aircraft design were chosen and used as inputs to a combination of surrogate and physics based models that were solved using fixed point iteration. Using range, endurance, climb rate, and aircraft mass as metrics, the problem was optimized using a sequential unconstrained minimization technique (SUMT) with an extended interior penalty function using a simplex optimization search algorithm. Several design constraints were active at the optimal solutions for both range and endurance. Results showed that the design was primarily driven by design variables governing hydrogen storage. The analysis also showed that optimizing a design for energy density did not produce the best aircraft design for either long range or long endurance. With the same payload, aircraft optimized for range and endurance were much smaller and had better range, endurance, and climb performance than aircraft optimized for energy density.