He started the following season, helping Bradford to two clean sheets in their first three league games, before he suffered another injury, after half-an-hour of a 3–2 defeat to Aldershot Town. City were 1–0 ahead when Clarke went off with a calf injury which was due to keep him out for up to a month. However, after missing a Football League Trophy derby game with Leeds United, he made a quick recovery playing in City's next league game. He was sent off after only 12 minutes of a 3–1 victory against Grimsby Town on 24 October 2008. In March 2009, Clarke and striker Barry Conlon were both dropped for a game with Exeter City and punished following a breach of club discipline. Manager Stuart McCall said: "It's an internal matter and has been dealt with in the dressing room." In the following game, Clarke scored City's equalising goal, but they fell to a 4–1 defeat to Bournemouth, which prompted McCall to offer to resign if the side did not reach the play-offs.