Accurate estimates of intense rainfall that induce flash floods in urban areas are necessary for flood hazard preparedness. The city of Kuala Lumpur is frequently hit by flash floods after prolonged heavy storms, causing substantial damage to property and infrastructure, and disruptions to the socioeconomic activities of urbanites. The flood mitigation measures that have been implemented include the 2007 construction of the Stormwater Management and Road Tunnel (SMART), which diverts the flood water coming out of the Upper Klang Ampang catchment from entering the city prime areas. This study developed an integrated hydrological model of the catchment with input from radar rainfall to estimate the flood volume threshold value for SMART operation. The hydrologic and hydraulic modeling were performed using HEC-HMS with the HEC-GeoHMS tool to extract the hydrologic parameter information using GIS as input data for the catchment model. A radar processing system named RAINRATE AUTO V2 was developed to efficiently process raw radar data from the Subang radar and produce calibrated and gridded rainfall to the HEC-HMS flood estimation model for the Upper Klang Ampang urban catchment area. The results show promising performance regarding the use of radar rainfall, and there was an acceptable percent error in the peak discharge simulations. The advanced integrated system can be applied in managing flood risks at the catchment scale by efficiently estimating incoming flood events in the future.