A 100W proton exchange membrane fuel cell (PEMFC) system with a sodium borohydride (NaBH4) hydrogen generator was investigated for small unmanned aerial vehicles (UAVs). The performance of a cobalt-phosphorous/nickel foam catalyst was evaluated to determine the change in catalytic activity under real operating conditions. The response time increased owing to oxidation of the metals and accumulation of sodium; however, the catalyst remained active at high reaction temperatures. A NaBH4 hydrogen generator with the catalyst was developed for a 100 W PEMFC system. The hydrogen generation rate was stable for 3 h, and the conversion efficiency was 97.8%. Finally, a 100 W PEMFC system with the NaBH4 hydrogen generator was investigated for small UAVs. The maximum power and energy density of the PEMFC system were 95.96 W and 185.2 Wh/kg, respectively.