Koeman, elder brother of Feyenoord coach Ronald, joined Utrecht last July but lost key players Ricky van Wolfswinkel, Dries Mertens and Kevin Strootman during the transfer window.
Assistant Jan Wouters will take over from Koeman and negotiate with the club about a permanent stay as head coach, the club said.
Utrecht are 10th in the league with 12 points after nine matches and host Heerenveen on Saturday.
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