Wilson was born and educated at the Royal High School of Edinburgh, and after acting as secretary of the Edinburgh Society of Antiquaries, went to Toronto as Professor of History and English Literature. He was the author of Memorials of Edinburgh in the Olden Time, The Archeology and Pre-historic Annals of Scotland (1851), Civilisation in the Old and the New World, a study on Thomas Chatterton, and Caliban, the Missing Link, etc.
Daniel Wilson served as president of University College, Toronto from 1880–1892 and as the first president of the federated University of Toronto from 1890–1892. Ironically he opposed the federation of colleges, particularly that of Victoria College, as a "Methodist plot".
Sir Daniel. J. Wilson Residence at the University College in University of Toronto is named in his honor.