Born in Wakefield, West Riding of Yorkshire, Cooper's football career started in 1987, where he first appeared on the books of Bristol City as a trainee, but never made any first team appearances for the club. After two seasons with the Robins, Cooper moved on to Exeter City, managed by his father, in October 1989. He played 50 games and scored 12 goals for the south-western club, and during his time with The Grecians, Mark went on loan to Southend United, where he only made 5 appearances.