Wilson became the anchor of the Broncos' defense and earned five Pro Bowl selections. He was one of the fastest middle linebackers in the league, and was also very good in pass coverage. He passed the 100-tackle mark in five consecutive seasons, including 109 tackles (73 of which were solo) in 2004 to rank second on the Broncos. Wilson led Denver in tackles for the second consecutive year in 2003 with 128 tackles.
On December 3, 2006, Wilson suffered a neck injury during a fake field goal attempt against the Seattle Seahawks during the Sunday night game. He was carted off the field and immediately taken to a hospital, but was cleared by the Denver Broncos to return the following week to help Denver try to make the playoffs.
The Denver Broncos signed many free agents during the 2007 offseason, such as Travis Henry and Patrick Ramsey, resulting in some salary cap trouble. The Broncos attempted to trade Wilson to the New York Giants, however Wilson failed his physical and the trade talks died down.
Wilson was released by the Denver Broncos on April 13, 2007, due to injuries and salary cap problems.
Wilson was cleared to return to resume playing by Los Angeles back specialist Bob Watkins in January 2008. On February 12, he had his first visit of the offseason with the Detroit Lions. He also visited the Cleveland Browns in March, but he rejected their offer for close to the veteran minimum.
Wilson officially announced his retirement on September 10, 2008.