Year 2005 came out to be a crucial year for Rolfes, with Bayer Leverkusen signing him and since then he has become a fan favorite, quickly winning a regular spot and not much after, captaincy in the full squad. He appeared in 37 matches in the 2005–06 season, 49 in the 2006–07 season, 47 in the 2007–08 season, and 39 in the 2008–09 season. Rolfes suffered a serious knee injury on 2 July 2009. During the 2009–10 season, Rolfes missed matchdays 10 to 17 and made his final appearance on matchday 19 against 1899 Hoffenheim. He made only 13 appearances in all competitions during the season. He missed out on the 2010 FIFA World Cup in South Africa. He returned to fitness the following season. He appeared in 36 matches in all competitions. He continued to be a regular late into his career. He made 40 appearances in the 2011–12 and 2012–13 seasons, 43 in 2013–14 season, and 33 in the 2014–15 season. On 7 December 2014, he announced his decision to retire from football after the 2014–15 season.