Clark has been the driving force behind the development of the Sixers since being appointed in May 2011 and helped guide the team to win the first BBL trophy last year before clinching last month's Champions League in South Africa.
"The last two years have been a great experience for me and I thank everyone at Cricket New South Wales for the opportunity," Clark said
"I never started out believing I would ever be a cricket administrator forever and now look forward to the exciting opportunity of moving into the corporate world.
"I have no immediate plans once I have finished with Sydney Sixers and will look at every possible avenue that is put in front of me."
Cricket NSW chief executive David Gilbert hailed Clark's contribution and said he was a key figure in the success of the Sixers.
"The remarkable success of the Sydney Sixers in its short history is testament to Stuart's ability to build a winning team," Gilbert said
"He has made a smooth transition from player to administrator and is well placed for the next phase of his career.
"Whilst it is disappointing to lose a person of Stuart's calibre, I understand and respect his decision and wish him the very best for the future.
Clark will finish with the Sixers in May at the conclusion of his current contract.