The 53-year-old took the reins in January 2010 and led the team to the runners-up spot in the K. League that year.
Jeju finished fifth at the end of the 2014 campaign and on Wednesday announced that Park has stepped down for health and personal reasons.
"It has been an unforgettable five years with Jeju," Park said.
"I have stepped down as manager but anytime Jeju need me I will be there."
Park is the second K. League managerial departure in the space of four days, after Ulsan's Jo Min-gook stepped down on Sunday, with Yoon Jung-hwan announced as his successor.