Traffic congestion has become a serious problem in many Asian developing cities; there is no exception for Phnom Penh. As urban areas continue to expand, more roads and intersections are built to accommodate the increasing traffic. The poor design of an intersection and traffic signal could be the roots of interrupting traffic flow and creating traffic conflicting areas which increasing traffic congestions in the city. In particular, one of the worst intersections in Phnom Penh is Kdan Pir intersection, which has been criticized for its poor geometry and traffic signal operations and its serious congestion levels, especially during the morning and evening peak hours. This study investigates the possible re-engineering alternatives to improve the traffic flow and reduce traffic congestion at Kdan Pir intersection. Six alternative options, including surface re-configuration, underground tunnels, and flyovers, were developed. The alternative options were analyzed in a micro-simulation environment using data from a traffic count survey at Kdan Pir intersection, between 7:00 and 20:00 on 04 November 2019. Results from each option were technically compared using the queue length, the mean travel time and the number of vehicle trips arrived, as the key indicator. The best options were also discussed in terms of short, medium, and long-term solutions for Kdan Pir intersection.