Urban flooding has emerged as a significant problem in fast-growing urban cities, with uncontrolled growth of impervious surfaces and overwhelmed drainage systems as the primary causes, leading to impaired stormwater management and flood susceptibility. The present study aims to analyze the main stormwater drain from Pumpwell to Jeppinamogaru, Mangalore, which flows into the Nethravathi River and then into the Arabian Sea. This drain is the main conduit for stormwater runoff. Heavy rain events led to extreme flooding in the Mangalore area in 2018 and 2023, with the Pumpwell area being flooded due to the drainage system’s low capacity. This paper uses PCSWMM to simulate stormwater flow and Geographic Information Systems (GIS) to pre-process input data. The extreme rainfall events were modeled in PCSWMM to evaluate flood conditions, which were calibrated using historical flooding records from these rainfall events. The stormwater drain was then redesigned in the most critical areas to ensure that the drainage network could manage the stormwater load effectively. Research is included in the broader project to enact structural and non-structural interventions to ease urban stormwater flooding, providing information on good flood mitigation policies.