During the Younger Dryas event, about 12,000 years ago, the Northern Hemisphere cooled by between 2 and 10 °C (refs 1, 2) whereas East Antarctica experienced warming. But the spatial signature of the event in the southern mid-latitudes and tropics is less well known, as records are sparse and inconclusive. Here we present high-resolution analyses of skeletal Sr/Ca and 18O/16O ratios for a giant fossil Diploastrea heliopora coral that was preserved in growth position on the raised reef terraces of Espiritu Santo Island, Vanuatu, in the southwestern tropical Pacific Ocean. Our data indicate that sea surface temperatures in Vanuatu were on average 4.5 ± 1.3 °C cooler during the Younger Dryas event than today, with a significant interdecadal modulation. The amplified annual cycle of sea surface temperatures, relative to today, indicates that cooling was caused by the compression of tropical waters towards the Equator. The positive correlation in our record between the oxygen isotope ratios of sea water and sea surface temperatures suggests that the South Pacific convergence zone, which brings 18O-depleted precipitation to the area today, was not active during the Younger Dryas period.