Mackinnon joined King's College London, first as a lecturer in 1919 under Arthur Dendy; she was promoted to reader two years later. When Julian Huxley resigned as Chair of Zoology in 1927, Mackinnon stepped up to the role which held also the title of Professor, where she would remain until her retirement in 1949. In doing so, Mackinnon became the first female chair at King's College. Her department produced notable academics such as Francis Brambell. After retiring, Mackinnon worked on an undergraduate textbook, "An introduction to the study of protozoa". She fell ill before it was published, eventually dying from a stroke on 10 September 1956, so the book was completed and edited by R. S. J. Hawes.
