The growing concern about climate change and the contemporary increase in mobility requirements call for faster, cheaper, safer, and cleaner means of transportation. The retrofitting of fossil-fueled piston engine ultralight aerial vehicles to hydrogen power systems is an option recently proposed in this direction. The goal of this investigation is a comparative analysis of the environmental impact of conventional and hydrogen-based propulsive systems. As a case study, a hybrid electric configuration consisting of a fuel cell with a nominal power of about 30 kW, a 6 kWh LFP battery, and a pressurized hydrogen vessel is proposed to replace a piston prop configuration for an ultralight aerial vehicle. Both power systems are modeled with a backward approach that allows the efficiency of the main components to be evaluated based on the load and altitude at every moment of the flight with a time step of 1 s. A typical 90 min flight mission is considered for the comparative analysis, which is performed in terms of direct and indirect emissions of carbon dioxide, water, and pollutant substances. For the hydrogen-based configuration, two possible strategies are adopted for the use of the battery: charge sustaining and charge depleting. Moreover, the effect of the altitude on the parasitic power of the fuel cell compressor and, consequently, on the net efficiency of the fuel cell system is taken into account. The results showed that even if the use of hydrogen confines the direct environmental impact to the emission of water (in a similar quantity to the fossil fuel case), the indirect emissions associated with the production, transportation, and delivery of hydrogen and electricity compromise the desired achievement of pollutant-free propulsion in terms of equivalent emissions of CO2 and VOCs if hydrogen is obtained from natural gas reforming. However, in the case of green hydrogen from electrolysis with wind energy, the total (direct and indirect) emissions of CO2 can be reduced up to 1/5 of the fossil fuel case. The proposed configuration has the additional advantage of eliminating the problem of lead, which is used as an additive in the AVGAS 100LL.