The boy was the passenger in a car which was in collision with a van on Lough Shore Road at about 13:00 BST on Wednesday.
Police said the 23-year-old driver of the car and the 47-year-old driver of the van have been taken to hospital.
Their injuries are believed to be serious, but not life-threatening.
The boy has been transferred to the Royal Victoria Hospital in Belfast.
An 11-year-old boy is in a critical condition in hospital following a two-vehicle crash in Enniskillen, County Fermanagh.