He has managed for Twente (assistant manager, manager and technical director) and PSV Eindhoven (youth coach and assistant manager). In the summer of 2008, he took over as the head coach of Schalke 04. On 26 March 2009, Rutten was sacked as Schalke manager. On 17 April 2009, Rutten signed a contract as the new manager of PSV Eindhoven, for the season 2009–10. After the start in the 2009–10 competition Rutten did not lose 39 games in a row. On 12 March 2012 Rutten was sacked as PSV manager after a disappointing spell of the club where they lost to Twente (2–6) and NAC (3–1) in the Eredivisie and to Valencia (4–2) in the Europa League. After this deception Rutten was asked for in Arnhem, because Vitesse had just lost John van den Brom, who went to RSC Anderlecht. He now surprisingly successfully manages Vitesse. At the end of the season Fred Rutten was sacked by Vitesse, Rutten claimed he had no conflict with Vitesse clubowner Jordania.