The Istanbul giant, which finished runner-up in the Turkish Super League, ended Kocaman’s second spell as manager a year after he rejoined the club.
The announcement was made on the team’s official website by newly-elected club president Ali Koc.
“We have reached an understanding that our football team needs to open a new page in terms of leadership,” he said.
“I would like to thank both personally and on behalf of our board of directors Mr. Kocaman for all his services to the club.
“Aykut Kocaman will continue to have a special place in our hearts.”
Fenerbache finished behind rivals Galatasaray and were defeated in the Turkish Cup final by mid-table Akhisarspor.
Reports have linked PSV Eindhoven manager Philip Cocu with the vacancy in at the club.