Electric flight is of increasing interest in order to reduce emissions of pollution and greenhouse gases in the aviation field in particular when the takeoff mass is low, as in the case of lightweight cargo transport or remotely controlled drones. The present investigation addresses two key issues in electric flight, namely the correct calculation of the endurance and the comparison between batteries and fuel cells, with a mission-based approach. As a test case, a light Unmanned Aerial Vehicle (UAV) powered exclusively by a Polymer Electrolyte Membrane fuel cell with a gaseous hydrogen tank was compared with the same aircraft powered by different kinds of Lithium batteries sized to match the energy stored in the hydrogen tank. The mass and the volume of each powertrain were calculated with literature data about existing technologies for propellers, motors, batteries and fuel cells. The empty mass and the wing area of the UAV were amended with the mass of the proposed powertrain to explore the range of application of the proposed technologies. To evaluate the efficiency of the whole powertrain a simulation software was used instead of considering only level flight. This software allowed an in-depth analysis on the efficiency of all sub-systems along the flight. The secondary demand of power for auxiliaries was taken into account along with the propulsive power. The main parameter for the comparison was the endurance but the takeoff performance, the volume of the powertrain and the environmental impact were also taken into account. The battery-based powertrain was found to be the most suitable for low-energy applications while the fuel cell performed better when increasing the amount of energy stored on board. The investigation allowed the estimation of the threshold above which the fuel cell based powertrain becomes the best solution for the UAV.