Tourists discovered around 50 bones in the cave, the scene of a mass killing of members of the Macdonald clan in the late 16th Century, last year.
Initial tests suggested the bones dated to between 1430 and 1620, potentially placing them to the time of the massacre which wiped out almost the entire population of the island.
Dr Kirsty Owen, senior archaeology manager at Historic Environment Scotland, said further analysis has now confirmed the bones belonged to a single skeleton of an adolescent aged under 16.
It has not been possible to determine their sex or stature, Dr Owen added.
Further tests are to be carried out at Bradford University to shed more light on the diet and lifestyle of the person whose remains have been found.
Results of a post-excavation analysis carried out at the cave are now being finalised with further radiocarbon dates from materials due soon.
HES plans to return the remains to Eigg once all investigations have been completed.
Dr Owen added: “When post-excavation analysis has been completed we will discuss what happens next with the community on Eigg. The decision will be made jointly with them.”
Police were called to the cave, also known as Francis Cave, last October following the discovery of the remains.
No proactive searches have been made for further remain given the cave is now treated as a war grave.
The massacre on the island occurred around 1577
Up to 400 Macdonalds are said to have been killed by their Macleod rivals in one of Scotland’s most chilling episodes of clan warfare.
According to accounts, the murders were carried out after three young Macleod men were expelled from Eigg and tied up on their boats after seemingly harassing a number of local girls.
After the men returned to the Macleod seat of power at Dunvegan on Skye, retaliation was planned with the clan organising a trip to Eigg
The Macdonalds, aware of the approaching Macleods, hid in a large cave, now known as Massacre Cave, in the south of the island for some time.
The Macleods then lit a large fire of turf and ferns at the entrance of the cave with the smoke suffocating those inside.
Only one family managed to escape, it is said.