He refereed the 2003 FAI Cup final when Longford Town beat St Patrick's Athletic in Lansdowne Road.

He refereed the 2011 Setanta Sports Cup final in Tallaght Stadium between Shamrock Rovers and Dundalk.

His final appearance as a referee in the League of Ireland was on 25 October 2013, when his former club Cork City FC defeated St Patricks Athletic 4-2 in Turners Cross.

Kelly was appointed to the FIFA list in 2002 and he refereed his first UEFA Champions League match, which was a 1st Round qualifier between Tirana and Dinamo Tbilisi in June 2003.

Kelly has been a regular appointee to Europa League Group Stage games and has refereed in the Round of 32 in the competition on 5 occasions.

His final Champions League game came at the Allianz Arena in Munich where Bayern defeated Viktoria Plzen in 2013.

On 26 March 2019 Kelly was selected to be a Video Assistant Referee for the 2019 FIFA U-20 World Cup in Poland.