Minor and under-21

Duignan first played for Offaly as a member of the minor team during the 1986 Leinster Championship. He made his first appearance for the team on 24 May 1986 in a 2-08 apiece draw with Kilkenny. On 13 July 1986, Duignan lined out at full-forward when Offaly faced Wexford in the Leinster final. He was switched to midfield in the second half and ended the game with a winners' medal after the 4-07 to 1-05 victory. On 7 September 1986, Duignan was again selected at full-forward when Offaly qualified to play Cork in the All-Ireland final. He scored two points from play and claimed an All-Ireland medal following the 3-12 to 3-09 victory.^[3]

Duignan immediately progressed onto the Offaly under-21 team. He made his debut in the grade on 26 April 1987 when he scored a point in the 2019 to 0-03 defeat of Westmeath in the Leinster semi-final. On 10 May 1987, Duignan was held scoreless at left wing-forward when Offaly suffered a 4-11 to 0-05 defeat by Wexford in the Leinster final

On 17 July 1988, Duignan played in a second successive Leinster final when Offaly faced Kilkenny. Lining out at midfield, he ended the game on the losing side after a 3-13 to 2-05 defeat.

Duignan lined out in a third successive Leinster final the following year. Playing at right corner-forward, he top scored for Offaly with 1-05 and collected a winners' medal after the 3-16 to 3-09 defeat of Kilkenny. Duignan was switched to left corner-forward for the All-Ireland final against Tipperary on 10 September 1989. He was held scoreless throughout the 4-10 to 3-11 defeat.

Senior

Duignan was still eligible for under-21 grade when he was added to the Offaly senior team in advance of the 1987-88 National League. He made his debut for the team on 11 October 1987 when he lined out at left corner-forward in a 3-11 to 0-11 defeat of Laois. On 6 March 1988, Duignan was at midfield when Offaly secured the Division 2 title after a 1-13 to 3-04 defeat of Down. He was later included in the Offaly panel for the Leinster Championship and made his first appearance on 19 June 1988 when he scored two points from midfield in a 2-13 to 2-10 defeat of Dublin. On 10 July 1988, Duignan won his first Leinster Championship medal after again lining out at midfield in a 3-12 to 1-14 defeat of Wexford in the final.

On 9 July 1989, Duignan lined out at right wing-forward when Offaly qualified for a second successive Leinster final. He was held scoreless from play but was instrumental in setting up two goals for Mark Corrigan in the 3-15 to 4-09 defeat of Kilkenny.

Duignan lined out in a third successive Leinster final on 8 July 1990. Playing at right corner-forward he scored two points from play and collected a third successive winners' medal after the 1-19 to 2-11 defeat of Dublin.

On 12 May 1991, Duignan was selected at full-forward when Offaly qualified for their very first National League final. He scored three points from play and claimed a winners' medal as Offaly claimed their very first league title after a 2-06 to 0-10 defeat of Wexford.^[4]

After a period without success, Duignan lined out in his fourth Leinster final on 17 July 1994. Playing at left corner-forward he scored a point from play and collected his fourth winners' medal after the 1-18 to 0-14 defeat of Wexford. Duignan, who had been prone to injury, suffered ligament damage during that game and was dropped from the starting fifteen for the All-Ireland final against Limerick on 3 September 1994. He was introduced as a substitute for Daithí Regan, however, Offaly looked like losing the game when they trailed by 2-13 to 1-11 with just five minutes remaining. Two quick goals by Johnny Dooley and Pat O'Connor and five unanswered points secured a remarkable 3-16 to 2-13 victory and a first All-Ireland medal for Duignan.^[5][6][7]

Duignan overcame his injuries and was restored to the starting fifteen for the 1995 Leinster Championship. He won his fifth Leinster Championship medal on 16 July 1995 after scoring three points from play in the 2-16 to 2-05 defeat of Kilkenny. On 3 September 1995, Duignan lined out at left corner-forward when Offaly faced a Clare team who were making their first All-Ireland final appearance since 1932. He scored a goal from play but ended the game on the losing side after a 1-13 to 2-08 defeat.^[8]

On 14 July 1996, Duignan made his sixth Leinster final appearance of his career. He scored 1-01 from midfield but ended the game on the losing side after a 2-23 to 2-15 defeat by Wexford.

On 5 July 1998, Duignan was selected at midfield when Offaly faced Kilkenny in the Leinster final. He was held scoreless from play in the 3-10 to 1-11 defeat. Team manager Babs Keating subsequently resigned after describing the team as "sheep running around in a heap" and was replaced by Michael Bond for the All-Ireland Championship.^[9] On 13 September 1998, Offaly qualified for the All-Ireland final where they faced Kilkenny for the second time that season. Duignan scored two points from right wing-forward and collected his second All-Ireland winners' medal after the 2-16 to 1-14 victory.^[10][11] He ended the season by receiving a GAA All-Star.

Duignan made his eighth Leinster final appearance of his career on 11 July 1999. He scored a point from left corner-forward but ended the game on the losing side after a 5-14 to 1-16 defeat by Kilkenny.

On 9 July 2000, Duignan lined out at left corner-forward in his ninth Leinster final appearance. He scored a point from play but ended that game on the losing side after a 2-21 to 1-13 defeat.^[12] On 10 September 2000, Duignan was switched to left wing-forward when Offaly suffered a 5-15 to 1-14 defeat by Kilkenny in the All-Ireland final.^[13]

Duignan made just two appearances during the 2001 National League, however, he decided to retire from inter-county hurling before the start of the Leinster Championship stating "It was a very, very hard decision after all the years."^[14]