Thomas joined JJB in 1994 ahead of the company's float on the London Stock Exchange.
His departure comes six months after a board shake up at JJB which saw chief executive Tom Knight replaced by Chris Ronnie as well as the departure of non-executive director Roger Best. Littlewoods chairman David Jones has since joined the board as a non-executive director.
JJB said in a statement: "Consideration has been given for a number of years to Andrew's retirement date in light of A.7.2 of the Combined Code on Corporate Governance. It has been mutually decided that now is the most appropriate time for his retirement, particularly in view of the other changes to the board during the summer of 2007."