Flyovers are constructed to manage heavy through movement. However, traffic operations underneath a flyover remain unmanaged and often pose a major concern in developing countries with non-lane-based heterogeneous traffic. This may reduce the overall benefit of a flyover. An alternative intersection layout is proposed to improve traffic operations at the intersection underneath a flyover. The proposed layout segregates the traffic movements through effective channelization. A traffic island is also proposed in the middle of the intersection to facilitate concurrent right-turning movements. This layout helps in eliminating a signal phase and cuts down traffic cycle time by 40 %. A microsimulation-based traffic simulation model is developed for the evaluation of the proposed layout. The simulation model demonstrates effectiveness of the proposed layout. Average delay and average queue length are compared to measure the effectiveness. Traffic volume sensitivity analysis is conducted to estimate the capacity of the proposed layout. An intersection underneath a flyover along the Eastern Expressway in Mumbai is considered for the case study. The effectiveness of the proposed layout at the study location for varying flow level is evaluated by comparing average delay, average stop delay, average number of stops per vehicle, average queue length, and maximum queue length.