	Prior to the start of the campaign, Carlisle stated his belief that Burnley could avoid relegation back to the Championship. He was selected in the team to play Burnley's first top-flight match in 33 years on 15 August 2009, when the team were defeated 2–0 by Stoke City at the Britannia Stadium. He also played in the following match as Burnley recorded their first ever Premier League victory, a 1–0 win over reigning champions Manchester United at Turf Moor. During the early part of the season, he formed a defensive pairing with new signing André Bikey. He was reunited with Caldwell in the centre of defence for the 2–1 victory over Birmingham on 3 October 2009. In the away loss to Wolverhampton Wanderers on 20 December 2009, Carlisle suffered a groin injury which kept him sidelined over the Christmas period. After over a month out of the Burnley team with the injury, he made his first start under new manager Brian Laws in the 1–0 defeat to Bolton Wanderers on 26 January 2010. Although the team was relegated from the Premier League at the end of the season, Carlisle was one of several players offered a new contract, and he signed a two-year extension in May 2010.