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. 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. He ended the season by receiving a GAA All-Star.