After his retirement from playing Clarke became a part of the Ulster coaching system, helping to establish the province's academy system. He was promoted to assistant coach under his former teammate Mark McCall, and served in this role during Ulster's 2005–06 Celtic League title-winning season. Following this success Clarke was hired by the IRFU as an Elite Player Development Manager, a newly created role with the directive of developing young Irish players. He also served as head coach of the Irish under-20 team and the Irish 'A' side during his time with the union.