Their signature daisy logo will be displayed on the 23-year-old's golf bag for the duration of the Abu Dhabi HSBC Golf Championship.
When the competition ends on 20 January, the bag will be auctioned on the Rory Foundation website, with proceeds going to the NI Cancer Fund for Children.
It comes as part of the foundation's 'Six Bags Project', in which six different charities will have their emblems displayed on McIlroy's golf equipment during six tournaments.
The Holywood star said: "When I was younger my parents sacrificed everything to allow me to play the game I love.
"Having that support from my family gave me the opportunity to chase my dreams. But I know that every child is not so fortunate. My aim is that The Rory Foundation will support children's charities big and small around the world that try to give kids that helping hand."
Gillian Creevy from NICFC said she is "delighted" with Rory's support.
She said the money raised will go towards developing a new therapeutic centre for children and their families.
"We are so proud and honoured to be the first of six charities benefiting from The 6 Bags project," Ms Creevy continued.
"This association with Rory will not only have a significant impact on children and young people who look up to Rory and are inspired by him, but will also help to maintain Rory's very important links to Northern Ireland as he moves increasingly into a global circuit.
"Our aim is to create a brand new therapeutic centre for children and their families, any monies raised from being part of The 6 Bags Project will go towards fulfilling this dream".