The former Tennents brewery managing director was a member of the plc board, joining after Dave King and his allies took control in March 2015.
Chairman King stated that Gilligan had decided to resign in order to focus on his business and family life.
In a statement, Gilligan said: “I am proud to have played my part in helping the right people regain control of our fantastic club. It was a long struggle but words can never describe the joy and thrill of winning that critical EGM. That memory will remain with me forever.
“There is still much to do but I am confident that the board will not fail our supporters, whose never-ending loyalty drives our club forward, and I thank each and every one of you for the tremendous backing we have received. I am looking forward to returning to my place beside you every week.
“Finally, let me say it has been a privilege to serve this wonderful club and its supporters at boardroom level. It has been like living the dream and I am honoured to be able to say that I was deemed worthy to be a director of this Scottish institution and the greatest football club in the world.”
King added: “When I approached John to assist with the rebuilding exercise he unhesitatingly agreed to do so, despite the challenges this would demand of his time given his other extensive business, social and family commitments.
“After years of tireless effort, lobbying, and campaigning to turn Rangers’ fortunes around, John has taken the decision to step down knowing that much of what was required post regime change has already been achieved and that the outstanding requirements have been clearly identified by the board, who have the necessary action plans in place.
“John would now like to concentrate on business and family life, as well as simply being a fan again.”