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The money will go towards 'The Goal' project of a sports and medical centre at St George's Park in Burton, central England.
It was only last year that FA chairperson David Bernstein received a frosty reception from fellow delegates after calling, unsuccessfully, for the unopposed re-election of FIFA president Sepp Blatter to be postponed in order to allow rival candidates to emerge.
Relations between FIFA and most of English football nose-dived when England's bid to stage the 2018 World Cup attracted only one FIFA vote apart from the one cast by the FA.
But Bernstein, welcoming the funding, said in a statement on Wednesday that relations were thawing.
"This is fantastic news and reflects FIFA's commitment to raising standards within the game around the world and to our improving relationship with FIFA."
Blatter added: "Protecting the health of players is one of our key objectives and I am therefore very pleased that this project will be dedicated to a sports science and medical centre at such an emblematic location at St George's Park."
The FA also announced Wednesday it will fund bursaries for nine promising international coaches to study for the FA International Licence course under a new scheme.
Meanwhile FA and FIFA officials also signed a memorandum of understanding, similar to agreements made between the global governing body and the Spanish and German FAs, agreeing to share knowledge with FIFA member associations.
Jane Bateman, head of international relations at the FA, said: "The FA has a long history of developing football around the world.
"Like the new memorandum of understanding with FIFA, this bursary project opens our education programmes to the international football community and, in this case, will give a group of international coaches the experience of St George's Park in its inaugural year.
"These coaches come from diverse backgrounds and all have great potential as coaches in their countries. We are proud to be supporting them and to be playing a key part in their development."
