Fanning first came to prominence on the inter-county scene as a member of the Tipperary minor hurling team in the late 1990s. He won a Munster title in this grade in 1997, however, Tipp were defeated in the later stages of the All-Ireland championship. Fanning later joined the Tipperary under-21 side, however, he had little success at this level. In 2003 Fanning was a dual player with his native county. That year he lined out with the Tipperary senior footballers in their qualifier game against Donegal. Fanning made his competitive senior hurling debut as a substitute in a National Hurling League game against Wexford in 2004. He made his championship debut against Limerick later that same year, however, Tipp's championship hopes ended in defeat. In 2005 Fanning lined out in his first Munster final, however, provincial rivals Cork were victorious on that occasion. Tipp were later defeated in the All-Ireland quarter-final. In 2006 Fanning's side took on Cork in the Munster final yet again, however, Cork won the game once again. Tipp were later defeated in the All-Ireland quarter-final once again. Tipp began their 2007 championship campaign with an epic series of three games against Limerick. Fanning's side lost the second replay, however, Tipp later came through the qualifiers only to be defeated in a third consecutive All-Irelad quarter-final. In spite of a lack of championship success Fanning was presented with his first All-Star award.
On 5 September 2010, Fanning started at right half-back as Tipperary won their 26th All Ireland title, beating reigning champions Killkenny by 4-17 to 1-18 in the final, preventing Kilkenny from achieving an historic 5-in-a-row, it was Fanning's first All-Ireland winners medal.
On 1 November 2010, Fanning announced his retirement from inter-county hurling. 'Having had the great honour of winning an All Ireland senior hurling medal with Tipperary this year, I have decided to call time on my inter-county hurling career, I am very grateful to Liam Sheedy and his management and backroom team for all the encouragement and support they gave me. I want to thank all the players, We worked hard together but we also had great fun and I shall miss training and hurling with them.' he said in a statement.