Francis McDermott, 19, from Camphill Park in Newtownbutler, is accused of unlawfully killing 13-year-old Oisín McGrath from Belcoo on 9 February 2015.
He entered the plea during a hearing at Dungannon Crown Court.
A defence lawyer said they will conduct the case in a way that will minimise the pain for the McGrath family.
He said an "unusual set of circumstances led to the collapse and death of Oisín McGrath" and they wanted to examine the medical evidence in the case.
He said further expert analysis was required.
The court was told that a trial would be expected to last three weeks.
The judge said he would adjourn the case until 23 March 2017 before setting a trial date.
Mr McDermott, who is a university student, was released on bail.
Oisín was taken to hospital following an incident at St Michael's College in Enniskillen and his life-support machine was switched off four days later.
At the time Francis McDermott was a sixth former at the school.
A teenager accused of the manslaughter of a Fermanagh schoolboy who died following a playground incident has pleaded not guilty.