[5] Encouraged by the geologist and palaontologist Maria Gordon, Mackinnon studied botany and geology at the University of Aberdeen.

Afterward, she joined Milano Vlès to research at Station biologique de Roscoff in France, and then relocated to the Quick Laboratory, at the University of Cambridge, under George Nuttall.

[1] "An inspiring teacher, rapid but always lucid in exposition, she had a natural dignity and a touch of the grand manner which at all times commanded respect and attention and which could, on occasions, give devastating force to a well deserved reprimand.'"

[6] She worked in military hospitals in Liverpool and Southampton,[6][9] where she used her knowledge of protozoology to help diagnose amoebic dysentery and other infections[10] for the War Office.

[6] When Julian Huxley resigned as Chair of Zoology in 1927, Mackinnon stepped up to the role which held also the title of Professor.

[1] Between May 1917 and May 1918, Mackinnon worked at the University War Hospital in Southampton with William Fletcher from the Royal Army Medical Corps, focusing on the diagnosis and treatment of dysentery.

The pair focused on two forms of Shigella dysenteriae which had been identified by Simon Flexner and Kiyoshi Shiga.

They discovered that the Flexner bacillus could go into intermission and be undetectable for periods of four to five weeks, making it very difficult to say when someone was no longer a carrier.

[14][15] Mackinnon published over 40 academic papers,[1] primarily on parasitic species of protozoa (especially flagellates and sporozoa).