The former Netherlands international only acquired the role during the summer, but news broke last month that he had been given time off to recover from a stress-related illness.
He has now decided that the time is right to walk away, although he will remain with the club for the time being to assist his successor, which will reportedly be his former assistant Alex Pastoor.
"I worked hard at it, because I find being a coach a great and interesting job. I tried to put this off for as long as possible, but you reach a point where you say 'this is something that keeps coming back too often,' and then you have to make a choice," said Van Basten.
The 49-year-old has previously coached the Dutch national side, Ajax and Heerenveen.