Injury interrupted the start of his Pools career and, when he recovered, the form of Paul Smith on the left wing required somebody to play on the right to help the balance of the side. Clarke was handed a right wing slot and it was there that he would play the majority of his matches for Pools. Although his new role reduced his chances of scoring he did still chip in with a useful number of goals, including a hat-trick in a 7-1 demolition of Swansea City in April 2002.
Clarke missed just one league game in the 2002/03 season as Pools won promotion from the bottom tier, and was also a regular member of the first team throughout 2003/04. From that point onwards things took a turn for the worse, with a succession of injuries restricting his football. In the summer of 2007, having started just six league games for Pools in three seasons, Clarke was released.