	Later the same day, Carlisle signed for League Two club Northampton Town, managed by former Watford boss Aidy Boothroyd, on loan for the remainder of the season. He made his first start for Northampton in the 1–0 win over AFC Wimbledon at the Sixfields Stadium on 14 February 2012. Carlisle was appointed captain upon his arrival at the club and was a regular first team player, often playing alongside fellow centre-back Kelvin Langmead. He scored his first goal for the team in the 3–1 home defeat to Bradford City on 14 April 2012. Carlisle played 18 matches and scored one goal for Northampton during his three months with the club, making his final appearance in the final match of the campaign, a 1–1 draw away at Rotherham. He was released by Burnley in May 2012 after the expiry of his contract.