Kelly serves on the staff of the House of Missions in Wexford and is made vice-Rector of the Irish College in Rome in 1891. In 1894, he is made head of Irish College. Kelly also becomes a leader in the temperance movement.
Elected Archbishop of Achrida In Partibus Infidelium and coadjutor cum jure successionis of Sydney on July 20, 1901, Kelly is Consecrated Coadjutor Archbishop on August 15, 1901 at St. Joachim’s Church, Rome, by Cardinal Francesco Satolli.
Kelly succeeds to the See of Sydney on August 16, 1911 upon the death of Cardinal Patrick Francis Moran. Kelly continues his crusade for temperance in Australia. Fund-raising for schools is undertaken by Kelly, and it is estimated £12,000,000 is spent on scholastic and church properties from the time of Kelly’s arrival in Sydney until his death. St. Mary’s Cathedral is completed in 1928 and statues of Kelly and Moran stand in the main portal.
Kelly is named Bishop Assistant at the Papal Throne and Count of the Holy Roman Empire on June 25, 1926. Kelly dies in Sydney on March 8, 1940 at the age of 90. He is buried in the Kelly Memorial Chapel in the crypt of St. Mary’s Cathedral.