Rowntree will assist England's forwards coach John Wells, starting at the training camp in Portugal later this month.
He had been working as assistant coach with Leicester, where he made 398 first team appearances.
"I am sad to leave Tigers and part of me will always be Leicester but this was an opportunity I couldn't turn down," said Rowntree.
"The chance to work with John Wells, one of the finest coaches I have ever known, and the senior England set-up is very exciting. Hopefully I can make a valuable contribution as well as learn."
Rowntree will join Jon Callard, Nigel Redman, Mark Mapletoft, Ben Ryan and Simon Hardy at the national academy.
"I find coaching and mentoring young players very fulfilling and I am looking forward to my role in developing England's future players," he added.
Rowntree won 54 caps for England in an 11-year international career, which included the 1995 and 1999 World Cups.
He toured with the Lions to South Africa in 1997 and to New Zealand in 2005.
RFU Director of Elite Rugby Rob Andrew said: "We are delighted to have recruited someone of Graham's calibre.
"He has played at the highest level and made a big impression at Leicester Tigers this season.
"He is another example of the development of a quality English coach.
"He will be a valuable addition to the RFU National Academy structure and more immediately to the England coaching team. We are grateful to Leicester Tigers for releasing Graham immediately."