Pilot fatigue is being dealt with as an important issue in relation to aviation safety. Recently, as unmanned aerial vehicles capable of flying for 24 hours have been delivered to the Korean Army, it is judged that it is time to pay great attention to research on fatigue management of UAV pilots. This study was conducted to confirm whether the major pilot fatigue-inducing factors highlighted by previous research results have the same effect on long-endurance UAV pilots in the Korean Army. As a result of the study, the fatigue of the ROK Army UAV pilots was proportional to the increase in flight duty time, and it was possible to identify that the increased pilot fatigue limits the mission performance when the flight duty time exceeded 8 hours. It was confirmed that the fatigue of the pilot flying at nighttime was higher than that of the pilot who flew during the daytime even when flying the same time. Through this study, we identified the implications of the need for the Korean army to refine the pilot working hours management regulations and raise interest in improving welfare conditions to manage the fatigue of long-endurance UAV pilots.