David Sheepshanks is to step down from his other roles in order to concentrate on his position as chairman of the FA's National Football Centre at Burton.
On Thursday the FA board voted for Sheepshanks to continue as chairman of St George's Park, a position he has held since the project began in 2008.
Sheepshanks said: "I have decided to stand down from the FA, Football League and Ipswich Town boards in June.
"This will allow me to devote more time to chairing St George's Park."
Sheepshanks, who will also remain as chairman of FA Learning, the FA's educational arm, added: "With construction under way there is an enormous amount to be done over the next year to prepare for operational readiness.
"A coach education and training hub for English football and other sports, St George's Park will benefit the entire pyramid of the game from grassroots to elite, as well as the local community."
Sheepshanks was Ipswich chairman between 1995 and 2009 before he became non-executive member of the board.
He will remain at Portman Road as chair of the club's PLC and the Ipswich Town Football Club Charitable Trust.