Police were called to the area at about 20:30 BST on Thursday and the child was pronounced dead at the scene.
The Health and Safety Executive (HSENI) is investigating the cause of death, which is understood to have involved farm machinery.
The boy's death was the first of a child on a farm in Northern Ireland for almost three years, said the HSENI.
There were seven deaths on Northern Ireland farms in 2016 and six the year before, it added.
The last child to die in a farm fatality was in June 2014, when a boy died in a slurry tank accident near Dunloy, County Antrim.
DUP leader Arlene Foster said the news had shocked the close-knit farming community in Fermanagh.
Ulster Unionist MP Tom Elliott said the community would rally around the "very close" family.
"The family have lost a son, a grandson and a brother and that's something I'm sure they will find very, very difficult to come to terms with," he said.
Former Sinn FÃ©in agriculture minister Michelle Gildernew said the community of Maguiresbridge was "devastated".
The Methodist Church in Maguiresbridge is holding a special service at 19:00 BST, inviting people to come together and to pray for the family.
A four-year-old boy has died in an incident at a farm in Maguiresbridge, County Fermanagh.