	Carlisle signed for newly promoted League Two club York City on 30 August 2012 on a contract lasting until January 2013, having previously turned down a contract offer from Northampton. He made his debut two days later in York's 3–1 victory at home to Oxford United. On 19 November 2012, Carlisle re-signed for Northampton on loan until January 2013, when he would sign permanently, having made 14 appearances for York. He made his second debut the following day in Northampton's 3–0 home win over Morecambe. After making five appearances on loan, Carlisle completed his permanent move to Northampton on a one-and-a-half year contract on 4 January 2013. He played for Northampton in their 3–0 defeat to Bradford in the 2013 League Two play-off Final at Wembley Stadium on 18 May 2013.