After a short trial with Norwich City in February 1990, Clarkson began his career in non-league football with Northern Premier League club Fleetwood Town, with whom he spent one year.
He began his professional career with Dario Gradi's Crewe Alexandra in the Third Division whom he signed for on 15 October 1991 for a transfer fee of £22,500.
[1] He remained at Gresty Road for five years, clocking up almost a century of league appearances, and helped the club win promotion in the 1993–94 season.
In 2002, he spent a short time on loan at Bury before being released by Blackpool at the end of the 2001–02 season having scored 35 goals in 171 league games for the Seasiders.
[1][2] Clarkson was inducted into the Hall of Fame at Bloomfield Road, when it was officially opened by former Blackpool player Jimmy Armfield in April 2006.