Abstract In recent years the concept of “more electric aircrafts” has established itself increasingly and the electrical power systems for aircrafts are in progress. In this context, fuel cells represent a valid source of electric power for the advantages in terms of pollution emissions, noise reduction and fuel consumptions. In this study, the authors analyzed the feasibility, from the specific energy point of view, in using a PEM fuel cell power system as APU unit in a more electrical aircraft with respect to a battery system installation. The proposed fuel cell system has a modular architecture and consists of fuel cell stacks, air compressors, heat exchangers, compressed hydrogen tanks and auxiliary batteries. The analysis has been performed by applying a design methodology based on an optimization procedure concerning the size and the efficiency of each power system component in order to reach the maximum specific energy (higher than 500 W h/kg). Moreover, a “black-box”-type model of the power system has been developed to support the optimization methodology in the evaluation of its performance in terms of electric power production, heat production, auxiliary systems consumption and hydrogen consumption. Results pointed out the advantages of the PEM fuel cell application in a more electric aircraft; as a matter of fact for assigned mission requirements, according to the specifications defined in the Long Endurance Demonstrator (LED) project promoted by CIRA (Italian Aerospace Research Centre), the specific energy of the designed power system results to be equal to 0.51 kW h/kg. This value is very interesting if compared to the specific energy of commercial LiPo batteries characterized by 0.2 kW h/kg.