Reports emerged earlier this afternoon that the Yorkshire-born businessman intended to leave the club, whose assets he purchased following the outfit's fall into administration last year.
A statement from Rangers to the Stock Exchange said: "The company announces that Charles Green has notified the board that he wishes to step down as chief executive with immediate effect.
"Recent weeks have seen media interest in the circumstances surrounding the period prior to the acquisition of the club by the consortium led by Mr Green.
"Whilst Mr Green strenuously denies any wrongdoing, he has recognised that this negative publicity is a distraction and is detracting from the achievements and reputation of the club. As a result, Mr Green has informed the Board that he will leave his post with immediate effect and leave the company, following an orderly handover, by the end of May."
On his decision to step down, Green stated: "Recent events have undoubtedly been a distraction for both myself and all involved with Rangers and I feel that it is appropriate that I step down so that the club can continue to progress back to where it belongs at the pinnacle of Scottish football.
"I am very proud to have been associated with a club of the stature of Rangers and am proud of the achievements of the club during my tenure as chief executive. My thanks go to the Rangers fans, whose support has been tremendous during my time at the club."
The 59-year-old is under an independent investigation by the club over allegedly being involved in covert dealings with former Rangers owner Craig Whyte.
Green has also been accused of racially abusing his commercial director Imran Ahmed during a newspaper interview.