Sean, who retired from playing at the end if last season, joins the Glasgow & West team at Broadwood Stadium, Cumbernauld.
Scotland Sevens stalwart Mark Robertson also joins the Academy coaching team to develop the nation's top young rugby talent.
Stephen Gemmell, Head of Academy and Performance Programmes, said it was important to acknowledge that the academies - increasingly well-known for developing quality players - is also creating opportunities to develop coaches.
He said: "I'm pleased to see the progression of quality coaches Mike [Legget], Derrick [Scotland Sevens] and Kathryn [Gallagher] into new roles as the academy, which illustrates the excellent opportunities being created to develop staff as well as players.
"It's also of huge value to bring the knowledge and experience of Sean [Lamont] and Mark [Robertson] into the system as they transition from playing to coaching."