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Intraseasonal variation of rainfall extremes within boreal summer in the Indo-Pacific region is driven by the Boreal Summer Intraseasonal Oscillation (BSISO), a quasi-periodic north-eastward movement of convective precipitation from the Indian Ocean to the Western Pacific. Predicting the spatiotemporal location of the BSISO is essential for subseasonal prediction of rainfall extremes but still remains a major challenge due to insufficient understanding of its propagation pathway. Here, using unsupervised machine learning, we characterize how rainfall extremes travel within the region and reveal three distinct propagation modes: north-eastward, eastward-blocked, and quasi-stationary. We show that Pacific sea surface temperatures modulate BSISO propagation — with El Niño-like (La Niña-like) conditions favoring quasi-stationary (eastward-blocked) modes—by changing the background moist static energy via local overturning circulations. Finally, we demonstrate the potential for early warning of rainfall extremes in the region up to four weeks in advance.