Perrin began his coaching career at AS Nancy in 1983, as junior coach to Arsène Wenger. He built up a reputation as a talented young coach whilst at the club, and was appointed to run the club's academy. In 1993, Perrin had his first chance at management, taking over as manager of French National 2 club Troyes AC, quickly taking the club to Ligue 1 after three promotions in six seasons, and qualifying for the UEFA Cup. His side won the 2001UEFA Intertoto Cup on the away goals rule after a 4–4 draw at Newcastle United. In May 2002, Perrin signed a three-year deal to succeed Bernard Tapie as manager of Olympique de Marseille. He was dismissed in January 2004 with the team in sixth, having lost 9 of their last 15 games. Days after leaving the Stade Vélodrome, Perrin was linked to a number of managerial positions around Europe, including at Premier League club Southampton. However, in July 2004 he was named manager of Al-Ain in the UAE Pro League, and remained there for three months. On 7 April 2005, Perrin did move to the Premier League when he took over at Portsmouth; the club were in 16th place and four points above relegation with seven games to go. On 24 April his side beat rivals Southampton 4–1 in the South Coast derby, a result that contributed to Pompey staying up and Saints being relegated. On 24 November 2005 Perrin was sacked by Portsmouth, having won only twice all season. Perrin returned to Ligue 1 in May 2006, taking over a Sochaux side that had just finished 15th under Dominique Bijotat. On 12 May 2007 he won the Coupe de France against former team Marseille, on penalties after a 2–2 draw; it was the team's first win in the tournament since 1937. Perrin took over as manager of Olympique Lyonnais on 30 May 2007, after Gérard Houllier resigned earlier that month. In his only season, he led the club to a seventh consecutive Ligue 1 championship title, and retained the cup for the team's first double. He stepped down in June 2008 due to differences with the club's backroom staff. He was rumoured to take over the position of French national manager, but it was confirmed on 3 July 2008 that Raymond Domenech would remain in the position. On 11 November 2008, he became the new manager of Saint-Étienne, and was fired on 15 December 2009. On 1 June 2012, Perrin decided to leave Al-Khor Sports Club to take up the vacant Qatar U23 position. His first assignment was to lead the team at the AFC Under-22 qualifiers, however the team were unable to make the tournament after they were knocked out in the group stages of the qualification process. Despite this disappointment Perrin continued to lead them into the 2012 Under 23 Gulf Cup of Nations where the team fared considerably better reaching the semi-finals of the tournament and eventually coming fourth overall in the competition. On 20 December 2012, Perrin joined Al Gharafa and left just about two months after. In March 2013, he was appointed new head coach of Umm Salal to replace Bertrand Marchand. However, he resigned from his post on 30 September 2013. On 28 February 2014, he was named as new China national football team manager, replacing Antonio Camacho. On 5 March 2014, China qualified for the 2015 AFC Asian Cup in Australia. In the tournament, Perrin secured a 1–0 victory for China over Saudi Arabia and two another 2–1 victories over Uzbekistan and North Korea. China finished first in the group and qualified to knockout stage after 11 years, where they faced host country Australia in quarter-finals where they lost 0–2. In April 2018 Perrin was one of 77 applicants for the vacant Cameroon national team job. On 27 October that year, he replaced Didier Tholot as manager of Ligue 2 club AS Nancy. On 28 May 2019, it was confirmed, that Jean-Louis Garcia would be the new manager of the club from the upcoming season.
