Energy is the most important factor determining the performance of a small unmanned aerial vehicle (UAV) with a proton exchange membrane fuel cell (PEMFC) system because the mission capability of a small UAV is determined by the energy of its power source. For this reason, in this study, a new conceptual design process for a small UAV with a PEMFC system was investigated with respect to energy. The mission profile and requirements for the small (AV were first determined. Five reference aircrafts were selected based on mission requirements, and some input parameters were assumed for conducting analyses based on these reference aircrafts. A constraint analysis was conducted to determine wing loading and power-to-weight ratios. The wing loading and power-to-weight ratios were used for mission analysis to determine the design specifications of the small UAV. The effect of gravimetric power and energy densities of the PEMFC system on the designed UAV endurance was also investigated. Finally, performance targets of the PEMFC system were suggested for a long endurance mission of the small UAV. This study investigated a conceptual design process that can be widely used for the conceptual design of small UAVs with PEMFC systems.