Wilkinson joined Connacht for the 2006–07 season, and made his debut on 1 September 2006 in an away victory over Scottish side Border Reivers in the Celtic League, playing the full 80 minutes in a Connacht victory. He made his first European appearance for Connacht on 20 October 2006 against Harlequins in the 2006–07 European Challenge Cup coming on as a replacement. Wilkinson played in a total of 18 Celtic League matches in his first season, 16 of these coming as starts, and also played in five Challenge Cup matches. In the following season, Wilkinson continued to play regularly for the side. With the number of teams reduced to 10 for the 2007–08 Celtic League, Wilkinson featured in all 18 of Connacht's matches, with only one of these appearances coming as a replacement. As well as his appearances in the Celtic League, Wilkinson started all six of Connacht's games in the Challenge Cup.