Clarke made his first start of the 2006–07 season coming on as a 61st-minute substitute replacing Danny Adams, in a 2–0 loss away at Crewe Alexandra on 2 September.

He ruptured a ligament in his left knee during Huddersfield Town's League One home match against Carlisle United, on 14 October 2006 forcing him to sit out most of the 2006–07 season.

Clarke joined Conference Premier club Halifax Town on loan on 21 February 2008, in a bid to regain match practice.

[3] He made his debut the following day against Grimsby Town, when he came on as a first-half substitute for Omar Daley, following defender Matthew Clarke's sending off.

[5] With a number of injuries, Bradford extended his loan spell for a second month, with Huddersfield caretaker manager Gerry Murphy able to recall him at 24 hours' notice.

[10] After fighting his way back from injury, Tom picked up where he left off in the 2009–10 season enjoying his best run in the team in central midfield under Lee Clark during the 2009–10 campaign.

Clarke became the club's starting left back during the third quarter of the season due to injured Gary Naysmith March and April 2012 until he was himself pushed out of the team by Calum Woods.

[15] Clarke signed a new one-year contract, committing himself to the Huddersfield Town until the summer of 2013 on 28 June 2012 making him the longest serving current player at the club.

[18] On 5 August 2013 in only his second appearance for Preston, Clarke scored a magnificent late winner in the 87th minute to defeat Blackpool in a derby game at Deepdale.