A British team using ice-penetrating radar found the chasm, dubbed the Ferrigno rift, and determined it was about a mile deep, the BBC reported.
In the geological rift system new crust is being formed as the eastern and western halves of the antarctic continent are slowly separating, scientists said.
Reporting their finding in the journal Nature, the team said the canyon is bringing more warm sea water to the ice sheet, speeding up its melting.
Researchers towed an ice-penetrating radar kit behind a snowmobile as they traveled nearly 1,500 miles.
"What we found is that lying beneath the ice there is a large valley, parts of which are approximately a mile deeper than the surrounding landscape," Aberdeen University glaciologist Robert Bingham said.
"If you stripped away all of the ice here today, you'd see a feature every bit as dramatic as the huge rift valleys you see in Africa and in size as significant as the [U.S.] Grand Canyon."