Flight Lieutenant Wales, as Prince William is known in the Royal Air Force, piloted the rescue helicopter after an emergency message was sent out on December 15.
Sources have told this newspaper that when the Duke of Cambridge arrived in Northern Ireland the authorities were informed that he was on board and flying the helicopter and after stopping off at Aldergrove, the Royal father-to-be picked up the ill infant, along with his parents.
Since the little boy's hospital admission, prayers have been said in a number of churches throughout the county.
The sick child from Ballinamallard continues to be monitored by doctors.
A source close to the family has told The Impartial Reporter: "He is still an ill child and all our thoughts and energies at the moment is on making sure he gets better. We are thinking about him and praying for him, and we really appreciate all the prayers we have received so far."
Fermanagh and South Tyrone MLA Tom Elliott said: "When a baby is sick it is a difficult time for any family. We have been praying for him and his family for a number of weeks."
A spokesperson for the Belfast Health Trust has confirmed that Prince William was the pilot involved in the emergency airlift.
He is based at RAF Valley in Wales.