Morgan attended Penistone Grammar School and played Sunday league football for Hoyland Common Falcons. He began his career at Barnsley, and made his first team debut under Danny Wilson in a 6–0 defeat to West Ham United in a Premier League tie at Upton Park on 10 January 1998. He was one of three "Tykes" players sent off in a 3–2 defeat to Liverpool at Oakwell on 28 March after his arm appeared to make contact with Michael Owen's head. He ended the 1997–98 season with 11 Premier League and three FA Cup appearances to his name as Barnsley were relegated in 19th-place. He played 19 First Division games under John Hendrie's stewardship in the 1998–99 campaign, and was sent off in a 3–1 home defeat to Norwich City on 8 September.