This paper presents the model for the queue formation by a cluster of powered two-wheelers (PTWs) at signalised intersections during a red phase. The formation and discharging processes of such queues are critically associated with the capacity of an intersection having a high percentage of PTWs. The key variables affecting the queue formation process were identified with field data from the Tainan City in Taiwan using vehicular trajectories extracting techniques. The results of extensive data analysis reveal that such process can be captured with a Multinomial Logit Model (MLM). To verify the fidelity of the calibrated MLM, it was integrated into a traffic microsimulation system to visually evaluate its simulated patterns of formation and discharging. The results have demonstrated that the calibrated MLM is capable of replicating the observed queue formation patterns. The research findings offer some valuable information for capacity assessments and mix traffic microsimulation at intersections containing PTWs.