Perrin began his coahcing career as a coach under Wenger at AS Nancy in 1983. He impressed and was promoted to run the club's academy.
He was then appointed manager of Troyes AC, gaining three promotions in six seasons. This success caught the eye of Olympique de Marseille, and he was appointed manager there in 2002.
There then followed managerial positions at clubs across the globe, including Al-Ain in the UAE, Portsmouth FC, Lyon, Saint Etienne and Qatar.
On 28 February 2014 Perrin was appointed coach of the Chinese National Football Team. He led the team to the quarter-finals of the Asian Cup in 2014, finishing top of their qualifying group.