The Indian Ocean Dipole (IOD) impacts climate and rainfall across the world, and most severely in nations surrounding the Indian Ocean1-4. The frequency and intensity of positive IOD events increased during the 20th Century5 and may continue to intensify in a warming world6; however, confidence in future IOD changes is limited by known biases in model representations of the IOD7 and the lack of information on natural IOD variability prior to anthropogenic climate change. Here we use precisely dated and highly resolved coral records from the eastern equatorial Indian Ocean, where the signature of IOD variability is optimised, to produce a semi-continuous reconstruction of IOD variability that covers five centuries of the last millennium. Our reconstruction demonstrates that extreme positive IOD events were rare prior to 1960. However, the strongest event on record (1997) is not unprecedented as at least one event that was approximately 27% to 42% larger occurred naturally during the 17th Century. We further show that a persistent, tight coupling existed between variability of the IOD and the El Niño-Southern Oscillation during the last millennium. Indo-Pacific coupling was characterised by weak interannual variability prior to ~1590 CE which likely altered teleconnection patterns, and anomalously strong variability during the 17th Century that was associated with societal upheaval in tropical Asia. A tendency for clustering of positive IOD events is evident in our reconstruction, which together with the identification of extreme IOD variability and persistent tropical Indo-Pacific climate coupling may have implications for improving seasonal and decadal prediction schemes and managing the climate risks of future IOD variability.