The El Niño-Southern Oscillation (ENSO) is the main driver of interannual climate extremes in Amazonia and other tropical regions. The current 2015/2016 EN event was expected to be as strong as the EN of the century in 1997/98, with extreme heat and drought over most of Amazonian rainforests. Here we show that this protracted EN event, combined with the regional warming trend, was associated with unprecedented warming and a larger extent of extreme drought in Amazonia compared to the earlier strong EN events in 1982/83 and 1997/98. Typical EN-like drought conditions were observed only in eastern Amazonia, whilst in western Amazonia there was an unusual wetting. We attribute this wet-dry dipole to the location of the maximum sea surface warming on the Central equatorial Pacific. The impacts of this climate extreme on the rainforest ecosystems remain to be documented and are likely to be different to previous strong EN events.