The decision follows weeks of discussion between FA chairman Lord Triesman and Barwick over his role within the FA. Triesman is the FA's first independent chairman and has been responsible for looking at the way it is structured.
In a statement to the press, Barwick said: "I'm sad to be leaving, but it's in the best interests of all parties. I have always endeavoured to do my job with passion, decency and integrity, and I believe I am leaving a strong legacy for the future".
Barwick was appointed by the FA in November 2004 three months after a sex scandal forced out his predecessor, Mark Palios. He is the fourth chief executive the FA has lost in less than 10 years.
