He signed for Shamrock Rovers in June 2001. He made his debut at Bray on 12 August and scored his first goal against Dundalk on 18 January 2002. Scully captained Rovers during that season, when the club played in Richmond Park. He formed a partnership in defence with Terry Palmer, the Rovers central defender who would later captain the club. Scully led Rovers to the FAI Cup final that season, although he could not prevent Derry City winning the competition with a 1–0 win.