Reduced greenhouse gas emissions via improved energy efficiency represent the ultimate challenge for the energy economy of the future. In this context, fuel cells for power generation aboard aircrafts have a promising potential to effectively contribute to the greening of air transportation. They can simplify today’s aircraft comprising electric, pneumatic, and hydraulic systems toward a more electric airplane. Although they are not considered in the short term as an alternative propulsion system for commercial aviation, many efforts are being devoted to their use as auxiliary power units and even aiming to build a distributed power network that might alleviate duties of the engine driven generators. In addition they allow new functions such as zero emission during taxiing on ground and/or increase safety by replacing the emergency ram-air turbine (RAT) by a fuel cell based emergency power generator. The present paper focuses on the effort that Compañía Española de Sistemas Aeronáuticos (CESA) is putting into the development of an aeronautical fuel cell system based on a high-temperature PEMFC covering all aspects from fundamental research in materials and processes to final integration concepts as a function of different architectures. A great deal of time and effort has been invested to overcome the challenges of PEM fuel cell operation at high temperatures. Among the advantages of these systems are the enhancement of electrochemical kinetics, the simplification of water management and cooling, the recovery of wasted heat, and the possibility of utilizing reformed hydrogen thanks to higher tolerance to impurities. However, new problems arise with the high-temperature concept that must be addressed such as structural and chemical degradation of materials at elevated temperatures. One of the aeronautical applications, where a fuel cell has an important role to play in the short term is the emergency power unit. Weight and mechanical complexity of traditional ram-air turbines could be drastically reduced by the introduction of a hydrogen fueled system. In addition, the output of the fuel cell is aircraft’s speed independent. This means additional power supply in case of emergency allowing a safer landing of the aircraft. However, a RAT replacement must overcome the specific difficulties concerning the very short start-up times allowed and the heating/cooling strategies to quickly raise the temperature to elevated levels and accurately maintaining the optimum operating range once in service.