Pelous proved himself an inspirational captain for France since succeeding Fabien Galthié ahead of the 2004 RBS 6 Nations. Enjoyed immediate success after leading Les Bleus to the Grand Slam in his first year and followed that up with a second-placed finish in 2005.
Pelous also helped Toulouse win the European Cup in 2005 before missing the summer test matches with a serious knee injury. He returned to action in September and was back to help France to a 26-16 win over Australia in November. However, Pelous was handed a nine-week ban in the aftermath of that victory after being found guilty of elbowing Australia hooker Brendan Cannon.
He was slated to equal Philippe Sella's record of 111 caps for France in the opener of the 2007 Six Nations against , but was ruled out of the side due to an ankle injury. After he missed their second Six Nations tie against , he was ruled out of the entire Six Nations. After his injury troubles continued, hooker Raphaël Ibañez, who had filled in for him as captain during the 2007 Six Nations, was named as France captain for the 2007 Rugby World Cup, with Pelous as unofficial vice-captain. He finally earned his record-equalling 111th cap on 11 August 2007 at Twickenham against , and took the record by himself on 18 August in Les Bleus' return match against England at Marseille.
He ended his international career after the 2007 Rugby World Cup with 118 caps, 42 of them as France captain. The night after the 2007 Rugby World Cup final, he was recognized at the IRB Awards, receiving the International Rugby Press Association Special Merit Award.