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This study investigates the impact of the northward/northwestward propagating 30–60-day mode of the boreal summer intraseasonal oscillation (BSISO) on the extreme rainfall events in the Philippines during the June–September (JJAS) season from 1979 to 2018. The Philippines domain is divided into the three latitudinal regions: Luzon region (13°–22°N), Visayas region (10°–13°N), and Mindanao region (5°–10°N) to account for the regional differences in the timing of extreme rainfall events. The probability density functions of JJAS rainfall are skewed towards higher values relative to the non-BSISO days in BSISO Phases 6–8, Phases 5–7, and Phases 4–6 over the Luzon, Visayas, and Mindanao regions, respectively, during which the probability of extreme rainfall events at the 95th percentile increases by as much as 80% in some stations in these regions. Further analyses of the large-scale circulation features show that the increase (decrease) in the probability of extreme rainfall events is associated with enhanced moisture convergence (divergence) induced by the cyclonic (anticyclonic) circulation anomalies of the BSISO and appearance of multiple tropical cyclones. About 36% of the total extreme rainfall events over the Luzon region are associated with TCs during Phases 7–8. On the other hand, TCs contribute by no more than 24% in all phases over the Visayas and Mindanao regions, indicating less TC influence in these regions. This study is the first attempt to clarify the impact of the BSISO on the extreme rainfall events in the Philippines.