In this study, we design and fabricate a fuel cell system for application as a power source in unmanned aerial vehicles (UAVs). The fuel cell system consists of a fuel cell stack, hydrogen generator, and hybrid power management system. PEMFC stack with an output power of 100W is prepared and tested to decide the efficient operating conditions; the stack must be operated in the dead-end mode with purge in order to ensure prolonged stack performance. A hydrogen generator is fabricated to supply gaseous hydrogen to the stack. Sodium borohydride (NaBH4) is used as the hydrogen source in the present study. Co/Al2O3 catalyst is prepared for the hydrolysis of the alkaline NaBH4 solution at room temperature. The fabricated Co catalyst is comparable to the Ru catalyst. The UAV consumes more power in the takeoff mode than in the cruising mode. A hybrid power management system using an auxiliary battery is developed and evaluated for efficient energy management. Hybrid power from both the fuel cell and battery powers takeoff and turning flight operations, while the fuel cell supplies steady power during the cruising flight. The capabilities of the fuel-cell UAVs for long endurance flights are validated by successful flight tests.