Peyton's reasons for resigning are to 'pursue his other interests within the football industry,' a statement on the clubs official website said.
'I was very lucky to be able to return to Fulham as a coach two season's ago and I have thoroughly enjoyed my time at the Club," Peyton told www.fulhamfc.com
"I have a great affection for everyone at Fulham especially the fans who were always so good to me when I was a player here.
"I am sad to leave, but having spent many years coaching abroad, I now feel that it is time to consider my options once again on both the international and domestic footballing scene.
"I wish Chris Coleman and Fulham every success in the future."