The following season saw Wilkinson make 18 appearances in the Pro12, the new name given to the league, starting in 15 of the matches. That season also saw Connacht qualify for their first ever Heineken Cup, and Wilkinson played his first ever match at the highest level of European rugby away against Harlequins at the Stoop. He went on to start every one of Connacht's pool matches, including their first ever Heineken Cup win in the return match against Harlequins at the Sportsground. In the 2012–13 season, Wilkinson played 18 games in the Pro12. Connacht again qualified for the Heineken Cup, with Wilkinson starting in three of the province's six matches, and featuring as a replacement in another two.