Horne was born on 1 January 1848, in Campsie, Stirlingshire, the son of Janet (née Braid) and James Horne of Newmill, a farmer. He was educated at the High School, Glasgow, and the University of Glasgow where he studied under Lord Kelvin. He left university without graduating at the age on 19.
In 1867 he joined the Scottish Branch of HM Geological Survey as an assistant and became an apprentice to Ben Peach. The two soon became good friends and collaborators. Horne was involved in mapping the Central Lowlands. Horne was a logical thinker and writer, complementing Peach's skills of resolving the internal structure of mountains by looking at the surface rocks. Thia approach allowed them to resolve a long-running debate on the geological formation of the Highlands. After their work in the Highlands, Horne and Peach wrote 'Northwest Highlands Memoir' in 1907. The work is regarded as one of the most important geological memoirs. Horne wrote most of the memoir himself. From 1901 until 1911, John Horne was the Director of the Scottish Branch of the Survey.
Horne was elected a Fellow of the Royal Society of Edinburgh in 1881, upon the proposal of Sir Archibald Geikie, Sir Charles Wyville Thomson, Peter Tait and Robert Gray, and won the Society's Neill Prize for 1889-92. Horne was very active in the affairs of the RSE and served as Councillor (1902-5; 1906-7; 1914-15), Vice-President (1907-13) and President (1915-19).
He died on 30 May 1928 in Edinburgh.
He was married to Anna Leyland Taylor (d. 1926).
A monument to the work of Peach and Horne was erected at Inchnadamph, close to the Moine Thrust where they did some of their best-known work. The inscription reads: "To Ben N Peach and John Horne who played the foremost part in unravelling the geological structure of the North West Highlands 1883-1897. An international tribute. Erected 1980."