In the context of aviation sector decarbonization, fuel cell hybrid electric aircrafts are a promising alternative to conventional fuels, presenting opportunities for more sustainable and efficient flight. Hence, the present work is focused on an alternative powertrain architecture, wherein a proton exchange membrane fuel cell system cooperates with a lithium-ion battery to fulfil the electrical power demand of a turboprop-based aircraft. Particularly, a mathematical tool is proposed to evaluate both the components size and performance, while a degradation aware rule-based control strategy guarantees an effective power split between the hybridizing components. Such an energy management approach introduces an idling level and a rate limiter to mitigate degradation associated with start-up/shut-down and transient phases, respectively. Moreover, to have a reliable estimation of the vehicle’s fuel economy, while also guaranteeing the correct components dimensioning, the fuel cell system efficiency model accounts for the recent targets on the achievable power density. The methodology has been applied to a realistic mission profile and the validity of the proposed rule-based strategy, which relies on versatile control maps, has been confirmed via benchmarking against dynamic programming results. The use of such a reference optimal controller for validation purposes represented a novelty in the aviation field. Specifically, when considering an electrical degree of hybridization of 0.79, the dynamic programming outputs a fuel consumption 2% lower than the rule-based strategy, ensuring the effectiveness of the latter.