After his active career, Arnesen was first appointed assistant coach at PSV under
Bobby Robson from 1991 to 1993, and in 1994 he became the club's general manager. Arnesen spent ten years as director of football at PSV Eindhoven, and was credited with discovering major talents, such as Brazilian striker
Ronaldo and Dutch players
Jaap Stam,
Ruud van Nistelrooy and
Arjen Robben. In May 2004, Arnesen was brought to
Tottenham Hotspur, replacing
David Pleat. Arnesen was to function as the manager responsible for player transfers and scouting for new talent, while coach
Jacques Santini handled the daily training sessions and match setups - an arrangement identical to Arnesen's days as PSV manager. Things did not work out well, and Santini left within months, citing "personal problems" as his reason for leaving. Arnesen's original hire for assistant coach,
Martin Jol, was put in charge of the club. Arnesen was suspended by Spurs on 4 June 2005 for expressing a desire to move to rival club
Chelsea, after Chelsea allegedly made an illegal approach to sign him as manager. Arnesen was photographed aboard one of
Roman Abramovich's three luxury yachts on 22 June 2005, thus reinforcing Tottenham's compensation claim. Arnesen was recommended to Abramovich by
Piet de Visser. Later on, one of the reasons to end
José Mourinho's contract would have been that Mourinho did not want to engage with Abramovich's football consultants. On 24 June, both clubs announced that they had reached a financial settlement, later disclosed to be £5 million, but widely reported to be closer to £8 million, and Arnesen would move to Chelsea, filling in the role of head talent scout, in charge of discovering footballing talents. Arnesen has since played a key role in bringing
Salomon Kalou,
Florent Malouda and
Mikel John Obi to Chelsea. But the club has still pursued expensive purchases of established international players, rather than unearthing and developing young talent as hoped. On 27 November 2010, Chelsea announced that Arnesen had resigned as sporting director, and would be leaving the club at the end of the 2010–11 season. On 20 February, he decided to join
Hamburger SV for the foreseeable future as sporting director, instead of returning to Ajax. As sporting director of Hamburg, Arnesen took Chelsea youngsters to Hamburg like
Jacopo Sala,
Michael Mancienne,
Gökhan Töre,
Slobodan Rajković (all permanent) and
Jeffrey Bruma (on loan). On 10 October 2011, Arnesen took over the additional task of the head coach of Hamburger SV for just one match, before hiring and installing a permanent new coach with
Thorsten Fink. On 22 May 2013, Hamburg confirmed that Arnesen had agreed to depart from his role as sporting director at the club. Arnesen was with the club for two years, including a spell as interim manager. On 30 January 2014,
Metalist Kharkiv announced that Arnesen will take over the role of sporting director from 1 February 2014. This position was only held for a month, as Arnesen and Metalist agreed that Arnesen could leave the club, due to the ongoing violent political situation in Ukraine. Speaking on the official Metalist Kharkiv website, Arnesen said: "I want to thank everyone in "Metalist". I got acquainted with all staff during this short period and realized that true professionals and very nice people work in the club. Also I would like to apologize to the fans, but the circumstances were stronger than me. The situation in Ukraine forced me to make this choice. I want to wish everyone at Metalist and throughout the Ukraine all the best in these difficult times". On 27 May 2015,
PAOK announced that Arnesen would be the new sporting director of the club for the next three years. After nine months, it was announced that his contract was terminated. ==Honours==