This paper presents the experimental methods and test results of a hardware-in-the-loop simulation of the powerplant for a small-scale fuel-cell-powered unmanned aerial vehicle. In this study, the hardware associated with the powerplant, power train, energy storage, and control systems operates dynamically as a component within a realtime aircraft simulation routine. Control signals, electrical loads, and mechanical loads are applied to the hardware to emulate the conditions of operation of the unmanned aerial vehicle powerplant during flight. Experimental results from hardware-in-the-loop testing of the fuel cell power train are presented with uncertainty analysis and discussion. These results show new aspects of the performance of fuel cell unmanned aerial vehicle powerplants, including the powerplant performance during long-endurance missions, power train subsystem power consumption, and unmodeled fuel cell dynamics. A comparison of the measured powerplant performance to experimental results from the literature shows that the fuel cell powerplant can outperform advanced electrochemical energy storage and internal combustion powerplants at the scale of the hardware-in-the-loop aircraft.