Born in Cookstown, County Tyrone, Hughes came through the ranks at Newcastle United. He made his first team debut in the Camp Nou in a match between Newcastle and Barcelona on 26 November 1997, replacing Philippe Albert at half-time in a 1–0 UEFA Champions League defeat. His league debut came against Sheffield Wednesday on 10 January 1998, playing the entirety of a 2–1 defeat at Hillsborough. Although he featured in the earlier rounds, including the semi-final against Tottenham Hotspur at Old Trafford in the latter campaign as a 36th-minute replacement for the injured Steve Howey, Hughes was not included in Newcastle's squads for their FA Cup Final defeats in 1998 and 1999.