Though much of the skeleton was intact, it was missing its left foot and the lower part of its left leg, he explained.
After examining the remains, the researchers concluded the foot bones weren't missing from the grave, or lost in an accident — they had been carefully removed.
The remaining leg bone showed a clean, slanted cut that healed over, Maloney said.
There were no signs of infection, which would be expected if the child had gotten its leg bitten off by a creature like a crocodile.
And there were also no signs of a crushing fracture, which would have been expected if the leg had snapped off in an accident.
The person appears to have lived for around six to nine more years after losing the limb, researchers say.
Prehistoric foragers knew enough about medicine to perform the surgery without fatal blood loss or infection, the authors concluded.
Researchers don't know what kind of tool was used to amputate the limb, or how infection was prevented — but they speculate that a sharp stone tool may have made the cut, and point out that some of the rich plant life in the region has medicinal properties.
Also, the community would have had to care for the child for years afterwards, since surviving the rugged terrain as an amputee wouldn't have been easy.
This early surgery "rewrites the history of human medical knowledge and developments", Maloney said.
Before this find, the earliest example of amputation had been a French farmer from 7,000 years ago, who had part of his forearm removed.
Scientists had thought that advanced medical practices developed around 10,000 years ago, as humans settled down into agricultural societies, the study's authors said.
But this study adds to growing evidence that humans started caring for each other's health much earlier in their history, said Alecia Schrenk, an anthropologist at the University of Nevada, Las Vegas, who was not involved with the study.
"It had long been assumed healthcare is a newer invention," Schrenk said.
"Research like this article demonstrates that prehistoric peoples were not just left to fend for themselves."