There are written accounts of cannibalism at Jamestown from the time but historians had previously been sceptical.
Douglas Owsley, a forensic anthropologist at the Smithsonian National Museum of Natural History in Washington, said: "Historians have questioned, well did it happen or not happen? And this is very convincing evidence that it did. This does represent a clear case of dismemberment of the body and removing of tissues for consumption."
He said the "chops" made to the girl's body had been done with a hatchet or cleaver, and appeared to be the work of someone not skilled at butchering.
"The person is truly figuring it out as they go."
The girl, who has been called Jane, was probably already dead at the time, he said.
Researchers were able to use the skull to create a three-dimensional model of what her face might have looked like. They believe she was probably a maidservant or the daughter of a colonist.
The settlers arrived during what is thought to have been the worst drought in 800 years. There were accounts of people eating dogs, cats, rats, mice, snakes and shoe leather to stave off starvation. After the "starving time", only 60 out of hundreds remained at Jamestown.
George Percy wrote of a "world of miseries" that included digging up corpses from their graves to eat when there was nothing else. "Nothing was spared to maintain life," he wrote.
Captain John Smith, the colony's most famous leader, documented a case in which a man was executed for killing, salting and eating his pregnant wife.
Smith wrote: "One amongst the rest did kill his wife, powdered her, and had eaten part of her before it was known, for which he was executed, as he well deserved.
"Now whether she was better roasted, boiled or carbonado'd [barbecued], I know not, but of such a dish as powdered wife I never heard of."
- Telegraph Group Ltd, AP