According to a press statement, the move is the first step of a "new leadership model" at BAC that will see Micklem's co-artistic director David Jubb become sole artistic director and CEO.
Jubb was sole artistic director of the venue from 2003 until Micklem was appointed in April 2008, shortly after the venue was threatened with closure.
BAC also announced today it is looking to appoint a commercial and operations director, who will be part of the executive team, when current executive director Sarah Preece completes her contract in April 2013.
BAC chair Michael Day said: "David has shown enormous loyalty and commitment to BAC. He has worked with David and the Board to consider what will serve BAC best over the next three years. Throughout his time at BAC he has demonstrated true qualities as a leader and on behalf of the Board I would like to wish him every success for the future."
David Jubb added: "It has been a huge privilege and a pleasure to work with David as joint artistic director since 2008. I am proud of what we have achieved together and BAC owes David a huge debt of thanks for his transformative and passionate contribution to the organisation and the way we now think about the future of theatre."
Speaking about his departure, Micklem said he was "enormously proud" of his achievements during five years as joint artistic director. "I leave with great confidence in David Jubb's vision for the years ahead and hope to remain closely connected as these plans unfold. In the meantime, I’m looking forward to taking a break and to exploring other leadership roles in the arts."