Stewart made 14 league appearances in two years at Springfield Park before former Latics manager Harry McNally signed him for Chester City in August 1986.
Stewart was allowed to join Northampton Town in July 1994, but ended the season playing at Wembley Stadium for Chesterfield in the Football League Division Three playoff final against Bury (while on loan with the Saltergate club).
Stewart played for the Sandgrounders for three and a half years, making another trip to Wembley in the final of the 1997–98 FA Trophy (which ended in a 1–0 defeat to Cheltenham Town).
Stewart moved to fellow Conference side Hednesford Town in December 1999 and later played for such clubs as Bamber Bridge, Rhyl, Marine and Colwyn Bay.
In November 2020, he was named as temporary co-manager of West Ham United Ladies team following the departure of Matt Beard.