The manuscript presents the conceptual design phase of an unmanned aerial vehicle, with the objective of a systems approach towards the integration of a hydrogen fuel-cell system and Li-ion batteries into an aerodynamically efficient platform representative of future aircraft configurations. Using a classical approach to aircraft design and a combination of low- and high-resolution computational simulations, a final blended wing body UAV was designed with a maximum take-off weight of 25 kg and 4 m wingspan. Preliminary aerodynamic and propulsion sizing demonstrated that the aircraft is capable of completing a 2 h long mission powered by a 650 W fuel cell, hybridized with a 100 Wh battery pack, and with a fuel quantity of 80 g of compressed hydrogen.