Brown's assistant Archie Knox will leave the club at the end of the season.
Craig Brown told RedWeb: "Having reflected long and hard on the situation, I felt the time was right for me to step down as manager.
"I feel it is important this is out in the public domain as I do not want anything to distract from the playing side over the next few weeks.
"Archie and I are determined to do whatever we can to help the team finish 2012-13 on a high and we strongly believe we will be leaving a solid base for the next management team to build on."
Brown will now 'move upstairs' to take a non-executive director's role at the club.
Club chairman Stewart Milne said: "When Craig indicated that he, would step down I asked him to become a non executive director and I am delighted to say this will take effect immediately."