And they did so without the benefit of the medical advances, researchers said.
Excavating burial caves in the south-central Andean province of Andahuaylas in Peru, University of California, Santa Barbara bio-archaeologist Danielle Kurin and her research team unearthed the remains of 32 individuals that date back to the Late Intermediate Period or 1000-1250 AD.
Among them, 45 separate trepanation procedures were in evidence.
According to Kurin, trepanations first appeared in the south-central Andean highlands during the Early Intermediate Period 200-600 AD, although the technique was not universally practised.
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"For about 400 years, from 600 to 1000 AD, the area where I work - the Andahuaylas - was living as a prosperous province within an enigmatic empire known as the Wari. For reasons still unknown, the empire suddenly collapsed," she said.
And the collapse of civilisation, she noted, brings a lot of problems.
Kurin's research shows various cutting practises and techniques being employed by practitioners around the same time. Some used scraping, others used cutting and still others made use of a hand drill.
"We can tell a trepanation is healed because we see these finger-like projections of bone that are growing," Kurin said.
It could take several years for the bone to regrow, and in a subset of those, a trepanation hole in the patient's head might remain for the rest of his life, thereby conferring upon him a new "survivor" identity.
When a patient didn't survive, his skull (the practice of trepanation on women and children was forbidden in this region) might have been donated to science, so to speak, and used for education purposes, researchers said.
"As bio-archaeologists, we can tell that they're experimenting on recently dead bodies because we can measure the location and depths of the holes they're drilling," she said.
The findings appear in the American Journal of Physical Anthropology.