Hydrogen is seen as a potential energy carrier for the next generation of aircraft that will be more climate-friendly than the previous generation of kerosene-powered aircraft. Two types of hydrogen-based propulsion systems are currently foreseen for such aircraft: hydrogen combustion and hydrogen fuel cell. In addition to producing useful electrical power, fuel cell systems produce a considerable amount of heat which must be removed to ensure the continued and efficient operation of the fuel cell stack. This thesis presents a thermal management system sizing methodology for propulsive fuel cell systems onboard CS-23 commuter aircraft. The developed methodology is implemented into an aircraft sizing environment to study the characteristics of air-based thermal management systems and their effects on aircraft design and aircraft performance. The results show that the thermal management system, through its additional mass, parasitic drag and parasitic power, has both a direct and indirect effect on aircraft performance. In addition to the conventional thermal management system, an unconventional system using nanofluids is studied. The use of nanofluids showed no considerable improvement in both system and aircraft level performance when compared to the base fluid. This thesis shows the importance of considering the design of thermal management systems during the conceptual design of fuel cell aircraft.