The 65-year-old has been in the role for over 10 years, restructuring the FA's development division and playing a key role in the establishment of the National Football Centre.
"I believe now is the right time to step away from my full-time role at The FA and I feel extremely positive about the future of Football Development moving forward," Brooking said in a statement.
"We have now put in place a strong, credible, elite structure to support the professional game."
Brooking, a technically gifted footballer and fine passer of the ball, played over 600 games for West Ham United and 47 times for his country before working as a commentator for the BBC and as chairman of Sport England.
"I watched Sir Trevor as a player and admired greatly his talent and commitment to his only club West Ham United." FA chairman Greg Dyke said.
"We've been lucky to have benefited from his vast experience and The FA has undoubtedly gained from this.
"His great legacy will be the development of the Skills programme, which now has over 160 full-time coaches working to teach children the benefits of playing football for fun."
Brooking is with the England squad in Miami preparing for this month's World Cup in Brazil.
"Trevor is a football man and has been a great friend to me," England manager Roy Hodgson said.
"He was a fine footballer, one that any England team would be grateful of and he has proven to be equally adept in his role at The FA."
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- West Ham United