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Extreme precipitation over the Maritime Continent (MC) is not only vital for local livelihoods, but also influences atmospheric circulation in tropical and extra‐tropical regions. The warm (cold) phase of El Niño‐Southern Oscillation usually leads to dry (wet) condition around the MC in boreal winter. This study unravels that extreme precipitation occurs in Borneo during both El Niño and La Niña winters. Extreme precipitation in Borneo is associated with tripole and dipole anomalous vertical motion pattern, respectively, over the MC‐tropical Pacific in El Niño and La Niña years. A parallel analysis reveals that weak precipitation in Borneo in El Niño and La Niña years occurs with dipole and tripole anomalous vertical motion pattern, respectively, over the MC‐tropical Pacific. The amplitude of the equatorial central‐eastern Pacific sea surface temperature (SST) anomalies may be a factor in the change of anomalous vertical motion pattern over the MC‐tropical Pacific. Further analysis identifies a tendency of extreme precipitation in late December to early−mid January and weak precipitation in February in Borneo. This suggests a critical role of seasonal change in the eastern equatorial Pacific SST in the occurrence of extreme precipitation in Borneo. Plain Language Summary: Extreme precipitation in the Maritime Continent (MC) is crucial for local communities and weather and climate beyond. El Niño‐Southern Oscillation is a mode of interannual climate variability in the tropical Pacific Ocean, with its warm phase (El Niño) leading to dry condition in the MC during boreal winter. This study reveals that extreme precipitation occurs in Borneo during both El Niño and La Niña winters with distinct anomalous atmospheric circulation patterns over the MC‐tropical Pacific. There is a tendency for extreme precipitation in Borneo to occur from late December to early−mid January and for weak precipitation in February. This study illustrates the modulation of El Niño and La Niña on Borneo's winter extreme precipitation and the role of seasonal sea surface temperature change in the equatorial eastern Pacific in shaping precipitation in Borneo. Key Points: Extreme precipitation occurs in Borneo during both El Niño and La Niña wintersExtreme precipitation is associated with distinct anomalous vertical circulation over tropical Pacific during El Niño and La Niña wintersSeasonal sea surface temperature change in the eastern equatorial Pacific has a crucial role in extreme precipitation in Borneo [ABSTRACT FROM AUTHOR]