The remains of a female in her late teens found in the upper layers of the ancient site were not buried in a recognised graveyard or in a traditional manner.
The woman, who was around 18 or 19 years old, is thought to have died in the 15th or 16th century.
The circumstances of her burial have led experts to wonder if she may have been killed.
"This person wasn't laid out on their back in an east-west direction, which is normal for a Christian burial," excavation director Dr Nora Bermingham explained.
"The body seems to have been bundled into position it was buried in.
She added: "It's not uncommon for people who have either committed crimes or people who have been murdered or what not to have been buried in this fashion."
Dr Bermingham said the cause of death may be discovered once the remains are examined by a bones specialist.
The woman would have been alive as the crannog, thought to be 1,400 years old, was coming to the end of its time inhabited by people.
More than 4,000 artefacts have been found at the crannog, which is an artificial island in a lake, revealing a "snap-shot" of life in Ireland from the 17th century back as far as the 9th century AD.
Carbon dating has confirmed that some of the site's earliest structures were laid down around 670 AD, with experts believing some remains could be older.
A unique wooden bowl with a cross carved into its base, parts of wooden vessels with interlace decoration, exquisite combs, a large pottery collection, "chess like" pieces for games, and timber foundations for dozens of houses are among some of the items uncovered.
Dr Bermingham has said the project is the "pinnacle of my archaeological career".
As the team of archaeologists have now completed the dig, the site will be concreted over this week as part of the A32 road project.