In January 2010, Ferguson signed as manager of Preston North End. His first game at home as a manager was an FA Cup match against Chelsea on 23 January 2010 which his side lost 2–0. On 14 September 2010, Ferguson was charged with misconduct by the FA after his behaviour in the tunnel towards the referee after a 4–3 Championship defeat by Burnley. After 49 games in charge, winning 13, drawing 12 and losing 24 games, he was sacked as manager on 29 December 2010, with Preston North End bottom of the Championship.