Electrification of aircraft is on track to be a future key design principal due to the increasing pressure on the aviation industry to significantly reduce harmful emissions by 2050 and the increased use of electrical equipment. This has led to an increased focus on the research and development of alternative power sources for aircraft, including fuel cells. These alternative power sources could either be used to provide propulsive power or as an Auxiliary Power Unit (APU). Previous studies have considered isolated design cases where a fuel cell system was tailored for their specific application. To accommodate for the large variation between aircraft, this study covers the design of an empirical model, which will be used to size a fuel cell system for any given aircraft based on basic design parameters. The model was constructed utilising aircraft categorisation, fuel cell sizing and balance of plant sub-models. Fifteen aircraft categories were defined based on the primary function and propulsion method of the aircraft. For each category, propulsive power and electrical generation requirements were calculated. Based on the results from categorisation and the flight envelope of the aircraft, fuel cell and balance of plant systems are defined. The total system mass and volume are given as outputs, along with polarisation and power curves for the fuel cell. This study finds that the model can accurately predict the electrical generation capability and propulsive requirements across the defined aircraft categories. In addition, the model can appropriately define key, high-level fuel cell parameters based on current Polymer Electrolyte Membrane (PEM) technology. Total fuel cell system mass and volume are calculated and shown to be reasonable for small aircraft. For larger aircraft with a Maximum Take-Off Weight (MTOW) greater than 50,000kg, current PEM technology is not able to match the gravimetric power density of existing APUs.