"He has told the club that he has decided not to extend his contract and that he will be leaving at the end of the season," Heerenveen said on their website (www.sc-heerenveen.nl).
The club made several efforts to discuss a contract extension with the 49-year-old former Netherlands striker, a three-time European Footballer of the Year and later national team coach.
"In recent weeks, at the request of the club, there were several discussions held between club management and Marco van Basten about the possibility of extending his contract.
"But he told the club he did not have the same feeling. The club management regrets his decision but, at the same time, naturally respects it," the Heerenveen statement added.
Van Basten signed a two-year deal with the club in 2012. Last season they finished eighth and they are now fifth.
His coaching career began with Ajax Amsterdam's reserves in 2003 but a year later he was named Netherlands coach, staying from 2004 to 2008, after which he spent a year at Ajax. He was then out of the game for three years before joining Heerenveen.
Last month Van Basten told reporters he had no desire to coach outside the Dutch league but his decision to leave Heerenveen is likely to alert clubs across Europe and prompt speculation about more attractive offers for the next campaign.