Shanahan made his debut on the inter-county scene at the age of seventeen when he first linked up with the Waterford minor team.
Shanahan represented the Munster inter-provincial team at various times throughout his career, winning one Railway Cup medal in 2007.
Shanahan was only sixteen years-old when he won a senior county club championship in 1993 following a one-point defeat of Passage.
[9] He had announced his retirement at the conclusion of the season, playing his last game for Lismore against Mount Sion in the Waterford SHC quarter-final.
The following year Shanahan and Waterford were back in the Munster final against the same opposition, and once again it was the Cork men who emerged victorious.
A star studded Midleton CBS outfit were the opposition, and despite Shanahan being amongst the goals, it was the east Cork school who took home the cup.
That year Waterford held All-Ireland champions Clare to a draw in the Munster final, however, the Decies lost the replay.
Shanahan's side later faced Kilkenny in the All-Ireland semi-final in what would be the county's first appearance in Croke Park since 1963.
In 2002 Waterford emerged from the doldrums by reaching the Munster final once again, however, Shanahan could not command a definite place on the starting fifteen.
[13] After surrendering the Munster title to Cork in 2003, Shanahan's side were back in the provincial showpiece for a third successive year in 2004.
In spite of this there was some consolation at the end of the year as Shanahan's scoring prowess earned him his first All-Star award.
In 2007 Shanahan added a National Hurling League medal to his collection when Waterford defeated Kilkenny by 0–20 to 0–18 in the final.
In spite of this poor start Shanahan's side reached the All-Ireland final for the first time in forty-five years.
In August 2010 he announced his retirement from the inter-county game after Waterford's exit to Tipperary in the All Ireland semi final.