On 16 May 2007, Cooper was appointed manager of Kettering Town. He had a successful first season with the Poppies, winning the Conference North title with a margin of 17 points. In the 2008–09 season, he guided Kettering to the FA Cup fourth round, a joint record for the furthest the club have been in the competition, where they faced Premier League team Fulham. He also guided the Poppies to eight place in the Conference National, completing a successful return to that division.