The former Netherlands striker took charge of Heerenveen ahead of the 2012-13 campaign, leading the club to an eighth-placed finish in his first year at the helm.
Heerenveen currently sit fifth in the Dutch top flight, but Van Basten has revealed he will walk away in May.
"Coach Marco van Basten has informed Heerenveen that he has decided not to renew his contract with the club," read a statement on Heerenveen's official website.
"The board regrets his decision, but has to respect this course."
A prolific striker during his illustrious playing career, Van Basten coached the Netherlands between 2004 and 2008 before leading Ajax for a solitary season.
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