This study investigates the interannual, seasonal, and intraseasonal variation in rainfall extremes (REs) in Jakarta and surroundings. We used datasets of daily rainfall at three sites with different altitudes at coastal, inland and mountainous environments during 1974-2016 (43 years), Sea Surface Temperature, Outgoing Longwave Radiation during 1979-2016 (38 years), and C-band Doppler radar data during 2009-2012 (4 years). Current results show that the interannual variability modulates the variation of seasonal REs. For example, intensity and frequency of REs, and their relative contribution to the total rainfall, have strong relationships with the Indian Ocean Dipole and El Niño Southern Oscillation in the dry season (Jun-Nov) but weak relationships in the wet season (Dec-May) at all sites. This study also finds the seasonal dependence on REs with the Madden-Julian Oscillation (MJO). During the active MJO period, the daily average rainfall and the number of RE days relative to all days show strong variation between MJO phases at all sites and the MJO signature differs between the three stations. At the coastal and inland sites, there is a less marked variation of the number of RE events relative to all days with MJO phases. Altitudes may play a role in increasing the number of RE events relative to all days in the wet season and decreasing the intensity of REs relative to total rainfall amount in the dry season. This study will also show the diurnal peak of REs, their spatial distribution and relationships with MJO from radar reflectivity.