Career
After returning from Middlesbrough he signed for Shamrock Rovers in October 2000 but never played for the first team and soon signed for Stephen Kenny at his home town club, Longford Town. He made his League of Ireland debut on the 27th of March 2001 at Flancare Park against Kilkenny City. His main position was left back but he also operated on the wing as well as a number of defensive duties.
He made 4 appearances in the for Longford Town.
Prunty signed for Drogheda United on a three-year full-time contract in 2008 but had to retire almost immediately when a medical check uncovered a previously undetected heart condition. On 21 November 2008 a testimonial was held for Sean Prunty which featured a clash between Longford Town F.C. and a Longford Town Legends XI, featuring the likes of Stephen O"Brien, Paul McNally, Wesley Byrne and Graham Gartland.
Marco Tardelli and Johan Mjällby made appearances for Longford Town on the night.