This paper evaluates the potential of fuel cell technologies to enable sustainable aviation by transitioning the aircraft industry toward low-emission operations. A comparative analysis of six fuel cell types—Proton Exchange Membrane (PEMFC), Alkaline (AFC), Direct Methanol (DMFC), Molten Carbonate (MCFC), Phosphoric Acid (PAFC), and Solid Oxide Fuel Cells (SOFC)—is conducted, assessing their operational principles, advantages, and limitations in aerospace contexts. The study identifies specific applications for each technology: PEMFCs and SOFCs emerge as leading candidates for Unmanned Aerial Vehicles (UAVs), regional aircraft, and Auxiliary Power Units (APUs), respectively, due to their power density, fuel flexibility, and compatibility with existing infrastructure. AFCs, while efficient, remain confined to controlled environments like space missions, while DMFCs offer logistical simplicity for low-power cargo drones. Key challenges include hydrogen storage complexities, where liquid hydrogen’s energy density lags fourfold behind conventional jet fuel, thermal management at high altitudes, power-to-weight ratio limitations, and high costs of precious-metal catalysts. Additionally, the need for new airport infrastructure for hydrogen production and refueling, alongside evolving safety regulations, underscores the systemic barriers to adoption. Current initiatives, such as Airbus’s ZEROe and ZeroAvia’s hydrogen-electric powertrains, signal incremental progress, with hybrid systems bridging transitional gaps. The paper concludes that widespread integration will likely commence with smaller aircraft and APUs, scaling to commercial fleets between 2035 and 2050. Sustained research, cross-sector collaboration, and investment are critical to realizing fuel cells’ role in decarbonizing aviation, aligning with global sustainability objectives while balancing operational efficiency and environmental stewardship.