In developing countries, motorcycle riders normally attempt to stop at their desired locations during queue formation on signalized intersection approaches. Under mixed-traffic conditions, motorcycle positioning in a queue affects the operational and safety performance of the intersection. This study aimed to identify factors influencing motorcycle riders’ stopping locations at signalized urban intersections. This study applied Unmanned Aerial Vehicles (UAVs) to observe the stopping behavior of 1413 motorcycle riders on 24 approaches from 10 signalized intersections in Thailand (N = 1413). Multinomial logistic regression analysis was used to determine the relationship between the stopping locations of motorcycle riders and rider- and motorcycle-related variables and traffic- and environmental-related variables. The statistical analyses presented a Cox and Snell R2 and Nagelkerke R2 of 0.466 and 0.499, respectively, indicating that the model accounted for almost 50% of the variation among the five stopping locations of motorcycle riders. The results showed that, under mixed-traffic conditions in Thailand with left-hand traffic, motorcycle riders intending to turn right, the morning peak period, the presence of shadows, motorcycle riders not wearing helmets, the presence of a larger vehicle in the queue, and the density of desired stopping locations significantly influenced the motorcyclists’ choice of stopping locations on signalized intersection approaches. Practical policy-related recommendations drawn from the findings are provided to improve motorcyclists’ safety on signalized intersection approaches.