David Moore, a senior academy coach, will also follow King to the Caribbean to take up the role of assistant coach with its national team.
Cricket Australia on Monday paid tribute to King's role in overseeing Australian cricket's player development system since taking up the head coaching position in 2002.
Academy Director Trevor Robertson said while it was disappointing to lose a key member of the academy's coaching panel, Cricket Australia offered its full support and congratulations to King.
"Over many years, Bennett King has made an outstanding contribution to the progress and development of Australias emerging players," Robertson said in a statement.
"In particular, his leadership and direction over the past two years in helping to establish the Commonwealth Bank Centre of Excellence is testimony to his capabilities as an educator and strategic thinker.
"Naturally its disappointing to lose someone of his calibre: his expertise, knowledge and dedication to the game are second-to-none.
"But this role is a wonderful opportunity for Bennett to demonstrate his skills as coach of a national team, and Cricket Australia understands his decision to take on this next challenge in his career."
Robertson said the academy will begin the search for a new leader to head the centre of excellence as well as a senior coach to work with coaching staff in John Harmer and former Test fast bowler Damien Fleming.
King joined the academy in 2002 after leading Queensland to two Sheffield Shield titles (1999-2000 and 2000-01) and two domestic One-day finals (1999-2000 and 2001-02) during his three-years at the helm.
King and Moore are expected to complete their roles at the academy in mid-November before taking up their positions with the West Indies.