On 19 October 1986, Duignan lined out at left corner-forward when St Rynagh's qualified to play Coolderry in the final.
He scored a point from play and was narrowly denied his first winners' medal after St Rynagh's suffered a 3-08 to 1-10 defeat.
Playing at right corner-forward, he was held scoreless throughout but ended the game with his first championship medal after the 0-11 to 0-09 defeat of Seir Kieran.
On 29 October 1995, Duignan lined out at centre-forward when St Rynagh's faced Seir Kieran in the final replay, having earlier missed the drawn match due to being on his honeymoon.
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.
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.
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 point from left corner-forward but ended the game on the losing side after a 5-14 to 1-16 defeat by Kilkenny.
[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.
[15] His opening season in charge saw Meath lose all of their National League games before suffering relegation to Division 2 at the end of the campaign.
On 17 April 2003, Duignan and his three selectors withdrew their services after the Meath County Board failed to fulfil a request to postpone a round of club matches in advance of a crucial league game against Antrim.
[16] The management team returned to their positions before the start of the Leinster Championship, however, Meath suffered a 0-17 to 2-10 defeat by Carlow.
[citation needed] In October 2019, it was confirmed that Duignan intended to run for the position of chairman of the Offaly County Board, after expressing strong criticism of the Executive over a number of years.