The 49-year-old guided the club to an eighth-place finish last season and, though they currently sit fifth in the Eredivisie, the former Netherlands striker will leave in May
The former Netherlands striker took charge ahead of the 2012-13 campaign, leading the club to an eighth-place finish in his first year at the helm.
Heerenveen currently sit fifth in the Dutch top flight but Van Basten has revealed that 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 the team's official website.
"The board regrets his decision but has to respect this [choice]."
The 49-year-old started his coaching career with Ajax's reserve side before spending four years as Netherlands boss and a single season at the helm of the Godenzonen, prior to his current position.