In October 2003, Deehan became Director of Football at Northampton Town, with Colin Calderwood working under him as team manager. The duo were appointed to get the team promoted from the league's basement division, and achieved this aim in the 2005–06 season. Both Calderwood and Deehan left the club at the end of the 2005–06 season, with Deehan moving to Lincoln City as Director of Football. On 15 October 2007, it was confirmed that Deehan and Lincoln City manager John Schofield had left the club. In November 2007, Deehan was employed as a scout by Premier League side Bolton Wanderers who were looking for a number of former professionals to head their recruitment drive led by former Everton manager Colin Harvey.