Born in Nova Scotia, Robert Aitken studied the flute with Nicholas Fiore at the Royal Conservatory of Music in Toronto. Following study with Frederick Wilkins and Julius Baker in New York, he met the eminent French flautist Marcel Moyse, whom he considers his principal teacher. In 1964, with a Canada Council grant, he studied in Europe with Jean-Pierre Rampal, Severino Gazzelloni, André Jaunet and Hubert Barwahser. At nineteen he became principal flautist of the Vancouver Symphony Orchestra and at 24 co-principal flautist of the Toronto Symphony Orchestra. In 1970 he left the orchestra to concentrate on composing and a solo career. He then founded and directed Music Today at Niagara-on-the-Lake (1968–70), the chamber music festival Music at Shawnigan (1981–1990) and was Director of the Advanced Studies in Music Programme at the Banff Centre for Fine Arts from 1985 to 1989.

Among his awards are the Order of Canada, the Roy Thomson Hall Award (Toronto), the Jean A. Chalmers National Music Award, the Chevalier de l’Ordre des Arts et des Lettres (France) and the Lifetime Achievement Award of the National Flute Association (USA). He was also a prizewinner in the Concours International de Flûte pour la Musique Contemporaine at Royan and the first Jean Pierre Rampal Concours International de Flûte de Paris.

Robert Aitken presents master-classes throughout the world, has more than fifty recordings to his credit and numerous composers have dedicated works to him. In 2004 he retired as Professor of Flute at the Freiburg Musikhochschule, a post he had held for sixteen years, to continue his solo and composition career and direct New Music Concerts (Toronto) which, with composer Norma Beecroft, he founded in 1971.