McCrum, who hailed from Milford, is famed for inventing the penalty kick in 1890, but his grave has fallen into serious disrepair and the estimated price for restoring it is £7,000.
Last week the Amalgamation handed over a cheque for £1890 to kick-start the fundraising campaign which was launched in the Ulster Gazette.
But on Saturday FIFA confirmed at the International Football Association Board press conference in Belfast, that they will pay for all of the repair bill.
Amalgamation chairman Gary McAllister said they were delighted that William McCrum will now have a grave befitting of a man that had such a major influence on the beautiful game.
“We made a tentative enquiry to FIFA and wrote to them about the McCrum grave and it was more in hope rather than expectation," said Gary.
“On Friday evening we received word that FIFA looked set to pay for the repair bill and that was confirmed at Saturday's press conference."
McAllister said that it has lifted a tremendous burden on the Milford NISC and the AoNISC and he confirmed that any funds already raised would go towards an event to promote William McCrum and the village of Milford following the complete restoration of the grave, which is in St. Mark's graveyard on Tower Hill, Armagh.
“We are hopeful of having an event to celebrate the restoration and we hope to work alongside the Milford NISC on how we can raise awareness of William McCrum and the impact that the penalty kick has had on football."
McAllister also said that a number of local businesses and groups had shown interest in donating money to the McCrum restoration fund and that any money already donated would be put to good use and used to promote and tell the story of Milford's most famous son.
Milford NISC member, Philip Johnston, said that it was a huge relief to hear that FIFA would cover the costs of the restoration.
“We are absolutely delighted with their decision and we would like to thank everyone who played a part in raising awareness about the William McCrum grave."
Speaking to the Ulster Gazette, following FIFA's decision, FIFA Vice-President, Jim Boyce, paid tribute to local Northern Ireland supporters, who have put so much time and effort into raising awareness of the need for immediate work on the McCrum grave.
“The local fans deserve a lot of credit for taking such interest in an initiative like the restoration."
“We were absolutely delighted to agree to pay and restore the William McCrum grave. FIFA acknowledge the contribution to world football by William McCrum and without him, there would be no penalty kick."