In June 2008, Paterson agreed a four-year contract with Burnley after being signed by manager Owen Coyle for a £1 million fee, which would rise to £1.3 million depending on appearances; the deal included a 20% sell on fee for Scunthorpe. He scored 19 goals in 57 appearances in the 2008–09 season, finishing as the club's top-scorer, as the "Clarets" reached the semi-finals of the League Cup and won promotion into the Premier League via the play-offs. He played the full 90 minutes at Wembley Stadium as Burnley beat Sheffield United 1–0 in the play-off final.