Hughes played a number of matches at various youth levels for Northern Ireland. He was first called up to the senior Northern Ireland squad in late 1984 but did not play for the team at that time. Following his performances for Bury, manager Billy Bingham included Hughes in the 22-man squad for the 1986 FIFA World Cup in Mexico. However, he was restricted to a place on the bench as Pat Jennings kept goal throughout the tournament. Jennings retired following the competition and Hughes became first choice goalkeeper. He made his international debut on 15 October 1986 in the 0–3 loss to England at Wembley. In the process, he became the only Bury goalkeeper to ever win international caps while playing for the club. He kept a clean sheet his second game for Northern Ireland as the side secured a 0–0 draw away at Turkey in a qualifier for UEFA Euro 1988. His final international appearance came on 18 February 1987 as the team drew 1–1 with Israel in a friendly. The shoulder injury he incurred playing for Wigan Athletic kept him out of the Northern Ireland setup and his place in the team was taken by George Dunlop.