Emission reduction is one of the challenges in the design of energy systems. This concern was already present in the aviation sector through the last decade, but now it is getting stronger as far as aviation is being included in the greenhouse gas trading system. In this sector, increasing fuel efficiency is considered the most effective mean of reducing emissions. Solid Oxide Fuel Cell hybridization with gas turbines was identified as a promising power generation system to substitute Auxiliary Power Units in airliners. The objective of this work is to present the physical, weight and cost models developed for simulating fuel cell and gas turbine hybrid systems for transportation applications. These models were implemented in WTEMP, original software developed by the Thermochemical Power Group of the University of Genoa. The analysis of two system layouts is conducted as case study. A promising system presented in literature is compared to a ‘simple cycle’ system, proposed in this work. Since it is characterised by a non-recuperated layout, its efficiency is lower, but this system has the advantage of being less expensive and more light-weighted than other systems being evaluated in open literature.