The rapid growth of unmanned aerial vehicles (UAVs) in infrastructure, agriculture, environmental monitoring, and emergency response has created increasing demand for platforms with extended endurance, operational autonomy, and minimal environmental impact. However, most current UAVs rely on lithium-ion batteries or internal combustion engines, both of which impose significant limitations in terms of range, emissions, and refuelling logistics. Hydrogen fuel cells offer a promising alternative, combining high energy density, zero emissions, and rapid refuelling, yet remain underutilized in practical UAV applications. This paper explores the potential of hydrogen-powered UAVs through the case study of HY-FLY, a vertical take-off and landing (VTOL) UAV designed around a dual PEM fuel cell architecture. With a 6-hour endurance, 440 km range, and rapid in-situ refuelling capability, HY-FLY demonstrates the technical feasibility and operational advantages of fuel cell propulsion. The UAV’s modular architecture, hybrid energy management, and low acoustic signature make it suitable for long-duration missions in remote or infrastructure-poor environments. A comparative analysis is presented between hydrogen, battery, and petrol UAV systems, supported by performance data, cost modelling, and sustainability metrics. Market insights and industry forecasts are also examined to position hydrogen UAVs within the emerging clean drone economy. The findings support hydrogen’s potential to enable a new class of sustainable aerial platforms, while highlighting current barriers related to infrastructure, regulation, and cost. Strategic recommendations are offered to guide future development and deployment in sectors where endurance, sustainability, and autonomy are critical.