The growing demand for air transport requires efficient and sustainable power systems to meet the pressing need for decarbonizing the sector. A hybrid unit, consisting of a proton exchange membrane fuel cell system and a lithium-ion battery, is a suitable option due to the advantages of reduced gravimetric and volumetric impacts, along with the flexibility of energy management strategies. This work addresses, using a model-based approach, the issue of integrating these electrochemical devices into the aircraft’s electrical architecture considering both design and energy management aspects. A literature derived DC-DC converter bi-dimensional power map is exploited to investigate scenarios differentiated by the fuel cell system power rating and number of stacks working in parallel such that the DC bus line voltage requirements can be respected. These maps relate the converter’s maximum deliverable power to the input and desired output voltage. The combined design and energy management problem is tackled via a multi-objective optimization supported by a design space exploration based on a full factorial parametric analysis. Therefore, a Pareto front is derived by considering the hydrogen consumption and overall hybrid unit mass as objective functions. As additional contributions, the auxiliaries’ power absorption, heat generated by the stack and resulting cooling load are also estimated, thus providing information for the preliminary sizing of the thermal management system. For the mission profile under consideration, the hydrogen consumption exhibited a variation ranging from 7 kg to 6.7 kg as the fuel cell system rated power increased. On the other hand, a smaller fuel cell system lowers the hybrid unit’s total mass. Particularly, when considering a configuration featuring a 70.5 kW fuel cell system, a single stack and two DC-DC converters, the total mass is estimated to be approximately 237 kg. Therefore, for the reduced impact on the aircraft’s maximal mass, the latter design choice is deemed as the most suitable option to be installed on hybrid aircraft with more electric onboard systems.