Kerr expressed his desire to leave Scarborough in June 2005 to return to the Football League and held talks with Barnet and Lincoln City. He opted to sign for Lincoln on a two-year contract on 1 July. He enjoyed an impressive debut season for Lincoln, under then manager, Keith Alexander, helping them reach their fourth successive play-off spot (albeit an unsuccessful one). The style of football played under Alexander, however, often undermined Kerr's ability as a midfielder, despite his presence being felt throughout the campaign. The 2006–07 season, however, under head coach John Schofield, meant that Kerr was able freely showcase his abilities. Kerr, as a consequence, formed a solid partnership with Lee Frecklington in the middle of the park for Lincoln, helping them in their promotion push for the fifth successive season.