Recurring outbreaks of leptospirosis in flood-prone areas caused by heavy rainfall pose a major public health concern, particularly in megacities such as Jakarta, Indonesia. From December 2019 through February 2020, Jakarta experienced a large leptospirosis outbreak due to extensive flooding following extreme monsoonal rainfall. We conducted a comprehensive retrospective analysis of the outbreak based on complete surveillance data from all five districts and 42 of 44 subdistricts in Jakarta. A total of 282 cases (97 suspected, 153 probable, and 32 confirmed) were reported in West (n = 162), South (n = 64), East (n = 30), North (n = 14) and Central (n = 12) Jakarta. Cases were predominantly adult males exposed to floodwaters. Of 241 cases tested, 164 (68.0%) had a positive IgM-based rapid diagnostic test (RDT). Of 118 cases tested with TaqMan RT-PCR targeting lipL32, 32 (27.1%) were positive. Of 95 cases tested with both assays, the combined detection rate was 74.7% (71/95); of whom 27 were positive by both RDT and RT-PCR. RT-PCR identified 5 additional RDT-negative cases, all of whom had fever <7 days. We sequenced 42 archived blood samples using Multi Locus Sequence Typing (MLST) and identified Leptospira interrogans and L. borgpeterseni as the predominant species. The findings emphasise the importance of rapid and early laboratory-based diagnosis during leptospirosis outbreaks in flood-prone urban areas, to better target public health interventions. Climate-resilient urban planning is critical for vulnerable megacities in low-resource settings, where complex environmental and infrastructural challenges are compounded by the effects of a changing climate.