The former prop, who joined Tigers in 1988 and went on to make 398 appearances for the club, worked as assistant forwards coach in the 2006/07 Double-winning season.
Rowntree, 36, replaces his former front-row colleague Dorian West at the National Academy and will assist John Wells, another ex-Leicester teammate, in the England camp. His first role will be at the senior training camp in Portugal this month.
A player popular with supporters and colleagues alike during a 16-year first-team career at Welford Road, Rowntree collected 54 England caps plus two with the British & Irish Lions after coming through the ranks at Tigers.
He made his final playing appearance for the club against Argentina in February and sits sixth on the club's all-time appearance list.
Rowntree said: "I am sad to leave Tigers and part of me will always be Leicester, but this was an opportunity I couldn't turn down.
"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 as National Academy coaches and he added: "I find coaching and mentoring young players very fulfilling and I am looking forward to my role in developing England's future players."
Richard Cockerill, Leicester Tigers' acting head coach until Marcelo Loffreda's arrival following the World Cup, said: "Graham has been a fantastic servant at Tigers and he was a very popular player over a number of years. We were happy that he took his first steps on the coaching ladder at the club he served so well as a player and we valued his contribution working with the squad.
"We are obviously sad to see him leave. However, this is a fantastic opportunity for him to further his coaching career in the national set-up and everyone at Welford Road wishes him well."
Rob Andrew, the RFU director of elite rugby, 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 coaching structure and, more immediately, to the England coaching team.
"We are grateful to Leicester Tigers for releasing Graham immediately."
