Perquis came up through the Troyes AC youth system. He played in Ligue 2 with Troyes AC for 2 years, where he was rated as one of the best defenders of the league. In 2005, he signed for Ligue 1 club AS Saint-Étienne as a free agent. In two seasons he failed to impress with the club and was loaned to Sochaux. After some initial troubles he finally found his form and became a regular in the starting line-up. In 2008 Sochaux bought the player outright. He made a total of 146 appearances for the club, scoring eleven goals, before leaving the club in the summer of 2012.
In the summer of 2012 Perquis joined Real Betis in Spain. He suffered through various injury problems while in Spain and was limited to 32 league matches in his three years with Betis. Perquis was released by Betis and signed with Toronto FC of Major League Soccer on 26 January 2015.
In December 2008 he declared his interest in playing for the Polish national team.Franciszek Smuda, manager of Poland, confirmed that information in July 2010. In January 2011, it was reported that Perquis had filed his citizenship application papers. However, his family had lost some required documents and so the Polish national team manager Franciszek Smuda had to request that the Polish president Bronislaw Komorowski approve his application. Perquis received Polish citizenship on 1 September 2011.
On 6 September 2011 Perquis made his international debut during a 2–2 friendly draw against Germany in Gdańsk. He scored his first goal on 26 May 2012, in a 1–0 friendly win against Slovakia.