Following his playing career, Rutten also managed Twente, before moving on to clubs like Schalke 04, PSV Eindhoven, SBV Vitesse, Feyenoord, Al Shabab, Maccabi Haifa and more recently Anderlecht.

On 12 March 2012, Rutten was sacked as PSV manager following losses to Twente (2–6) and NAC (3–1) in the Eredivisie and to Valencia (4–2) in the Europa League.

On 3 March 2014, Feyenoord released a statement confirming they had hired Rutten as their new head coach for the 2014-15 Eredivisie season.

On 2 March 2015, Feyenoord announced that Rutten had decided not to extend his one-year contract, meaning he would leave the club at the end of the season.

[3] On 20 May 2022 PSV confirmed that Rutten would return for the 2022-23 season as an assistant under head coach Ruud van Nistelrooy.