Wilson then signed for Dunfermline Athletic on 5 August 2002. He made his Dunfermline debut in a 6–0 defeat to his former employers Rangers, just two weeks later. Wilson played in the 2006 Scottish League Cup Final and the 2007 Scottish Cup Final, both of which ended in defeat to Celtic; his defensive colleagues included former Rangers youth teammate Greg Shields.
Wilson signed for Dunfermline Athletic on August 5, 2002. He made his debut for Dunfermline in a match against Rangers, his former team, two weeks later. Wilson participated in the 2006 Scottish League Cup Final and the 2007 Scottish Cup Final, both of which ended in defeat to Celtic; his defensive partners included Greg Shields, a former teammate from Rangers' youth academy.