Recent paleoclimate reconstructions have suggested millennial-scale variability in the Indo-Pacific Warm Pool region coincident with events of the last deglaciation. Here, we present a new stalagmite oxygen isotope record from northern Borneo, which today is located near the center of the region's mean annual intertropical convergence zone. The record spans the full deglaciation, and reveals for the first time distinct oxygen isotope variations at this location connected with the Bølling-Allerød onset and the Younger Dryas event. The full deglaciation in the Borneo stalagmite proxy reconstruction appears remarkably similar to a 20–11 ka transient simulation of rainfall over the area produced using the isotope-enabled Community Earth System Model. In this model, periods of weakened Atlantic Ocean meridional overturning circulation are associated with an anomalous Western North Pacific anticyclone, which is produced in boreal autumn and shifts south over Borneo during boreal winter, causing dry conditions.