After surrendering the Munster title to Cork in 2003, Flynn's side were back in the provincial showpiece for a third successive year in 2004. In one of the greatest games of all-time Waterford defeated Cork in a Munster final for the first time in forty-five years to take the title by 3–16 to 1–21. One of the highlights of a game that had everything was a Flynn goal from a close-in free. An All-Ireland appearance subsequently eluded the team yet again. In spite of this there was some consolation at the end of the year as Flynn won his sole All-Star award.