The Rebels were beaten 2-11 to 0-10 by three-in-a-row chasing Dublin in the All-Ireland semi-final at Croke Park and the Nemo club man confirmed that he'd be vacating the top job in Cork ladies football.
Fitzgerald guided Cork to an All-Ireland in his first season and earlier this spring got the better of the Dubs in the league.
"I originally planned to do three years in the job and I stayed on this year for a fourth. The result didn't influence my decision. I had my mind made up beforehand.
"I'd like to thank the rest of the management and everyone who was involved and helped during my time with this team. They're a very talented bunch and I know they'll bounce back to win more silverware, especially as the underage structures are very strong.
"It's been a wonderful experience. I hope now that whoever takes over will take on that challenge and take the team forward again.
"In a year or two they can get back up those steps in Croke Park again."
John Cleary, who has excelled as minor boss in recent seasons, and Tipp and Mourneabbey manager Shane Roynane will be leading candidates for the position.