He was born in Elgin on 13 February 1846, the son of John Alexander Cooper (d.1881), a local merchant and former farmer, and his wife, Ann Stephen of Old Keith (d.
[2] He also spent at least one semester at the University of Heidelberg before being licensed to preach as a Church of Scotland minister by the Presbytery of Elgin.
[3] After serving some time as assistant in various parishes, Banchory-Ternan, Stirling and Elgin, he was ordained as minister of St Stephen's Church in Broughty Ferry near Dundee in April 1873.
[3] In September 1898 he was presented under patronage of Queen Victoria to Glasgow University as Professor of Ecclesiastical History, beginning teaching in 1899.
[3] In 1917 Cooper was elected Moderator of the General Assembly of the Church of Scotland in place of John Brown.