Born in Greenock as James MacCunn, the son of a shipowner, he went to London in 1893 and was educated at the Royal College of Music, where his teachers included Sir Hubert Parry and Sir Charles Villiers Stanford. His first success was with the overture The Land of the Mountain and the Flood on 5 November 1887 atthe Crystal Palace, and this remains far and away his best-known piece. It was followed by other compositions, always with a characteristic Scottish colouring. From 1888 to 1894 McCunn was a professor at the Royal College of Music, where he had a long artistic association and friendship with Marmaduke Barton.
In 1888, he married Alison Pettie, daughter of John Pettie, RA, who had painted MacCunn's portrait several times. They had one son. John Pettie was an enthusiastic musician, who helped MacCunn build up his career by organising concerts of his work. It was at this point that Carl Rosa commissioned MacCunn to write an opera on a Scottish subject. The world premiere of his first opera, Jeanie Deans, conducted by the composer, took place at the Royal Lyceum Theatre in Edinburgh on 15 November 1894. He was for some years a conductor with the Carl Rosa Opera Company and subsequently to other companies. A hectic programme of composing, conducting and teaching brought about a gradual deterioration in MacCunn's health, and he died in 1916 aged only 48.