Meiolaniid or horned turtles are members of the extinct Pleistocene megafauna of Australia and the southwest Pacific. The timing and causes of their extinction have remained elusive. Here we report the remains of meiolaniid turtles from cemetery and midden layers dating 3,100/3,000 calibrated years before present to approximately 2,900/2,800 calibrated years before present in the Teouma Lapita archaeological site on Efate in Vanuatu. The remains are mainly leg bones; shell fragments are scant and there are no cranial or caudal elements, attesting to off-site butchering of the turtles. The new taxon differs markedly from other named insular terrestrial horned turtles. It is the only member of the family demonstrated to have survived into the Holocene and the first known to have become extinct after encountering humans.