Yogyakarta has increasing trends in the number of vehicles and consequently intensifying the traffic volume and will effect to higher emission and air pollution. Traffic lights duration plays a vital role in congestion mitigation in the critical intersections of urban areas. This study has objective to minimize the number of vehicles waiting in line by developing the hybrid simulation method. First of all, the MKJI and Webster method were calculated to determine the green traffic light. Then, the simulation model was developed to evaluate the number of vehicles waiting in line according to different duration of green traffic lights from MKJI and Webster method. A case study will then be provided in Pelemgurih intersection located in Yogyakarta, Indonesia for demonstrating the applicability of the developed method. The result shows that the duration of green traffic lights calculated by Webster method provides lower number of vehicles waiting in line. It is due to the short duration of green traffic light resulted by Webster method so that the traffic light cycle becomes shorter and it effects the number of vehicles waiting in line which is lower than MKJI method. The results obtained can help the generating desired decision alternatives that will important for Department of Transportation, Indonesia to enhance the road traffic management with low number of vehicles waiting in line.