While West Antarctica has experienced the most significant warming in the world, a profound cooling trend in austral summer was observed over East Antarctica (30°W to 150°E, 70° to 90°S) from 1979 to 2014. Previous studies attributed these changes to high-latitude atmospheric dynamics, stratospheric ozone change, and tropical sea surface temperature anomalies. We show that up to 20 to 40% of the observed summer cooling trend in East Antarctica was forced by decadal changes of the Madden-Julian oscillation (MJO). Both observational analysis and climate model experiments indicate that the decadal changes in the MJO, characterized by less (more) atmospheric deep convection in the Indian Ocean (western Pacific) during the recent two decades, led to the net cooling trend over East Antarctica through modifying atmospheric circulations linked to poleward-propagating Rossby wave trains. This study highlights that changes in intraseasonal tropical climate patterns may result in important climate change over Antarctica.