Subglacial outburst floods at the margins of the Antarctic and Laurentide Ice Sheets have been linked to changes in global ocean circulation and climate. The impact of palaeo-hydrological systems beneath the East Antarctic Ice Sheet (EAIS) has, however, remained elusive. By analysing bed morphology in the Wilkes Subglacial Basin, we hypothesise the occurrence of a major palaeo-subglacial lake and associated outburst floods in the interior of East Antarctica. At similar to 70 km wide and over 100 km long, the inferred area of outburst flooding is the most extensive in Antarctica, and the palaeo-subglacial lake from which the floods originated is the second largest after Lake Vostok. The scale of inferred outburst flooding is similar to mega-floods beneath the Laurentide Ice Sheet. We suggest that this major hydrological system developed during expansion of the EAIS in the middle Miocene and probably affected ice sheet stability, ocean circulation and climate evolution.