In recent years, civil aircraft projects are showing a continuous increase in the demand of onboard electrical power, both for the partial substitution of hydraulic or pneumatic controls and drives with electrical ones, and for the consumption of new auxiliary systems developed in response to flight safety and environmental control issues. Aiming to generate on-board power with low emissions and better efficiency, several manufacturers and research groups are considering the possibility to produce a relevant fraction of the electrical power required by the aircraft by a fuel cell system. The first step would be to replace the conventional auxiliary power unit (APU, based on a small gas turbine) with a Polymer Membrane fuel cell type (PEM), which today is favored with respect to other fuel cell types thanks to its higher power density and faster start-up. The PEM fuel cell can be fed with an hydrogen rich gas coming from a fuel reformer, operating with the same jet fuel used by the aircraft, or relying on a dedicated hydrogen storage onboard. The cell requires also an air compression unit, where the temperature, pressure and humidity of the air stream feeding the PEM unit during land and in-flight operation strongly influence the performance and the physical integrity of the fuel cell. In this work we consider different system architectures, where the air compression system may exploit an electrically driven compressor or a turbocharger unit. The compressor type and the system pressure level are optimized according to a fuel cell simulation model which calculates the cell voltage and efficiency as a function of temperature and pressure, calibrated over the performances of real PEM cell components. The system performances are discussed under different operating conditions, covering ground operation, intermediate and high altitude cruise conditions. The optimized configuration is selected, presenting energy balances and a complete thermodynamic analysis.