After coming through the All-Ireland series Cork reached the All-Ireland championship decider. For the second year in succession Galway were the opponents. Murphy produced a fantastic exhibition of hurling in that game, scoring 1–5, as Cork went on to win by 2–10 to 1–8. It was his first All-Ireland minor winners' medal. Murphy subsequently joined the Cork under-21 team, however, he enjoyed little success in this grade. He lost back-to-back Munster deciders to Tipperary in 2003 and 2004, with Murphy serving as captain in the former year. Murphy's performances at under-age levels brought him to the attentions of the Cork selectors at senior level. He made his senior championship debut in 2003, a year which saw Cork's players emerge from a bitter stand-off with the county board, however, he played no part in the county's Munster final victory and subsequent All-Ireland final defeat.  2004 saw Cork reach the Munster final once again and, for the second consecutive year, Waterford provided the opposition. In what many consider to be the greatest provincial decider of them all, both sides fought tooth-and-nail for the full seventy minutes. Unfortunately for Murphy, Cork lost the game by just a single point on a score line of Waterford 3–16, Cork 1–21. Although Cork surrendered their provincial crown they were still in with a chance of landing the All-Ireland title. After manoeuvring through the qualifiers Cork reached a second consecutive All-Ireland final and, once again, Kilkenny provided the opposition. This game took on a life of its own for a number of reasons. Chief among these was the fact that Kilkenny were attempting to capture a third All-Ireland title in-a-row and go one ahead of Cork in the All-Ireland roll of honour. The game was expected to be another classic; however, a damp day put an end to this. The first-half was a low-scoring affair and provided little excitement for fans. The second-half saw Cork completely take over. For the last twenty-three minutes Cork scored nine unanswered points and went on to win the game by 0–17 to 0–9 with Murphy knocking over two vital scores en route to victory. It was Murphy's first All-Ireland winners' medal. In 2005 Cork were on form again and the team won back the provincial crown that year with a 1–12 to 1–16 victory over Tipperary.