Donald Mackinnon was born in Kilchattan on Colonsay, in the Hebrides, on 18 April 1839. He was educated locally and then later, from the age of eighteen, at the Church of Scotland Training College, Edinburgh, which was apopular route to studying at Edinburgh University. Between 1860 and 1863 he was engaged as a school-teacher in Lochinver, Sutherlandshire, where he made a close study of the dialects and literature of the North Highlands. Mackinnon studied at Edinburgh University where he obtained the degree of M.A. in 1870. Earlier, in 1869, he had become Clerk to the Church of Scotland's Educational Scheme, and in 1872 he was Clerk to the Endowed Schools and Hospitals Commission.
After the passing of the Education Act, and on the formation of the School Board of Edinburgh, Mackinnon was appointed as its first Clerk and Treasurer. This was a difficult time to hold such a position because Scottish Education was in the transition stage from control by the Churches to control by elected bodies.
In 1882, he became the first Professor of Celtic at Edinburgh University, and he held the chair until 1914. His experience and acquaintance with the North Highlands served him in his capacity as member of the Crofters Royal Commission chaired by Lord Napier in 1883. Mackinnon's contribution to the Commission's Report was impressive enough to speed up subsequent legislation for the improvement of conditions for Scotland's crofters. Among his publications were the Reading book for the use of students of the Gaelic class at Edinburgh University (1889), and On the dialects of Scottish Gaelic.
Professor Donald Mackinnon died in Balnahard on Colonsay on 25 December 1914.