Following a break from football to obtain qualifications in accountancy, Gannon signed with Shelbourne in August 2001. Despite being appointed as captain upon his arrival, he initially struggled to get into the first team during the 2001–02 League Championship winning season, and considered a move back to England. However, he found himself a key member of the defence when new manager Pat Fenlon took over. Under Fenlon, Gannon helped the "Shels" to a second-place finish in 2002–03, and also played in the 2002–03 UEFA Champions League qualifying rounds, scoring past Hibernians in a 2–2 draw at the Ta' Qali National Stadium. He did not feature extensively in the club's 2003 League Championship winning side.