Long joined the Australian Imperial Force on 16 November 1917 as an Anglican chaplain. He sailed for London in January 1918 and was posted to the Australian Reinforcement Camp in France in April 1918. There he was approached by Major General Brudenell White to head the AIF's education project. Long accepted the post of Director of Education, AIF on 10 May 1918 and was promoted to lieutenant colonel on 1 June 1918. Long established himself in London, and drew up a scheme for professional, general and technical training to be conducted by teaching within the AIF and by sending men out to universities, schools and businesses. Officers with instructional experience were selected and assembled for three weeks training at the University of Cambridge. In three weeks at Cambridge, Kelly produced the books Beef, Mutton and Wool, the first of a series of fifteen texts written by Long's agricultural section.
Post war
When the war ended on 11 November 1918, Long was forced to put the education scheme into full effect earlier than expected. He was promoted to colonel and then temporary brigadier general on 1 January 1919. In March, with the scheme fully underway, Long's health began to suffer, and in April he handed over control to Brigadier General Walter McNicoll. For his services, Long was awarded honorary Doctor of Letters degrees by both the University of Cambridge and the University of Manchester, and was appointed a Commander of the Order of the British Empire. In July 1919, Long returned to his diocese, where he continued his involvement with education. He restarted All Saints College in Bathurst on a new site, and opened the Marsden School for Girls at Kelso. Long was grand chaplain of the United Grand Lodge from 1923 to 1926. He drafted a new constitution for the Church of England in Australia, making it independent of the church in Britain, and advocated the White Australia Policy. Long was elected Bishop of Newcastle in December 1927 and was enthroned on 1 May 1928. Long went to England in March 1930 to attend the Lambeth Conference in London. There he suffered a cerebral haemorrhage and died on 9 July 1930. His requiem was celebrated by Archbishop Cosmo Lang before 300 bishops and his ashes returned to New South Wales and placed in All Saint's Cathedral in Bathurst. He was commemorated in Christ Church Cathedral, Newcastle, where a window of its Tyrrel chapel contains his portrait.