Prunty began his career with Celtic, but he failed to make a senior appearance. In January 2004, he moved to fellow Scottish Premier League club Aberdeen,[2] making his senior debut in a Scottish Cup replay victory against Dundee on 21 January 2004.[3] His first senior goal came on 27 March 2004 in a 3–1 defeat against Kilmarnock.[4] At the end of the 2003–04 season, Prunty was told by manager Jimmy Calderwood that he could leave the club.[5]
Prunty spent part of the 2009–10 season on loan at Stirling Albion.[10] It was widely believed Prunty would sign permanently for Stirling in January 2010, but instead he was snapped up by Alloa Athletic.[11] Prunty scored on his Alloa debut in a 2–0 win over Stenhousemuir.[12]
On 16 May 2011, Prunty then joined Dumbarton.[13] In February 2012, he scored an overhead kick against Stenhousemuir which was voted as SFL Goal of the Month,[14] then a year later won the same award after scoring a stunning overhead bicycle kick from the edge of the box in a match against Livingston in February 2013, which was reported to have been viewed so many times it caused the Livingston club website to crash.[15] The goal was also voted Goal of the Season at both the PFA Scotland and Scottish Football League end of season awards.[16][17] On 16 May 2013, Prunty agreed a new one-year contract with Dumbarton.[18] In May 2014 Prunty agreed a new one-year deal with Dumbarton.[19]