In August 2010 he joined Stoke City in a deal which saw Stoke duo Liam Lawrence and Dave Kitson join Pompey. He converted to left back under Tony Pulis and in his first season at Stoke he played in the 2011 FA Cup Final as Stoke lost 1–0 to Manchester City. Wilson was a regular in 2011–12 as Stoke played in the UEFA Europa League. He suffered a broken leg in October 2012 which saw him miss most of the 2012–13 season. He became used as a back-up player under Mark Hughes and left Stoke in August 2016 to join Bournemouth.