The FA council has voted against allowing chairman David Bernstein to remain in the post beyond his 70th birthday.
Bernstein has been praised for his performance in the role since he replaced Lord Triesman in December 2010.
But he has been unable to get the FA Council to amend their statutes to allow him to continue in his job beyond next spring.
"I respect the decision and I remain committed to fulfilling my responsibilities and to building on what we have achieved over the past two years," he said.
"Next year is a significant one in the FA's history and I look forward to leading the organisation in the months ahead."
England manager Roy Hodgson said: "I have a very good relationship with David Bernstein. He is the person who appointed me and I have worked closely with him over my five months.
"I have really enjoyed that, have been really happy to work with him and will enjoy working with him until next July. But these are not decisions that are anything to do with me and football.
"I have really enjoyed that, have been really happy to work with him and will
enjoy working with him until next July."
"But these are not decisions that are anything to do with me and football. Decisions over whether he can stay on beyond his 70th birthday is a matter for the Football Association."