Saints confirmed Crocker was set to make the switch later this year after helping to establish the club's academy as one of the most recognised in England.
Welshman Crocker, who will work under the FA's new director of elite development Dan Ashworth, has worked at Southampton for seven years and at an academy that has produced the likes of Gareth Bale, Theo Walcott and Alex Oxlade-Chamberlain.
Crocker will be employed by the FA as its head of coach & player development and Saints executive chief Nicola Cortese admitted he would be missed on the south coast.
"Matt will leave us with the best wishes of everybody associated with the club," Cortese said in a statement.
"He has given Southampton seven years of hard work and dedication, and played an important part in developing the academy that we have today.
"Although we are sad to lose a talented member of staff, it is an honour to see the work of a Southampton employee recognised by the FA. We are ranked as the best academy for producing players for the English national teams, so it is no surprise that they have turned to Matt for this vital role.
"Matt will be hard to replace, but we expect serious interest from exceptional candidates who will be desperate to work for an Academy with a reputation such as ours."
Crocker will remain at Southampton and assist in the recruitment process for his successor before moving to the FA.
- Employment & Career
- Sports & Recreation
- Nicola Cortese