John Fergus qualified as Bachelor of Medicine (MB) and Master of Surgery (CM) at the University of Glasgow in 1875. After some time as acting house physician and house surgeon at the Royal Infirmary in Glasgow he qualified as Doctor of Medicine (MD) at the University of Glasgow in 1878. He came to the Cape Colony the same year, where he was licensed to practice on 1 June 1878. Settling in Tarkastad he practiced there to 1909, for many years as district surgeon of Tarka. By 1888 he owned two portions of farms in the district. During the 1890s and up to 1909 Dr William Henry Fergus (MB and CM, Glasgow, 1886), who may have been John's brother, also practiced in Tarkastad; he had returned there by 1916 as medical officer of health.
In 1903 John Fergus donated the skull of a Triassic reptile to the South African Museum in Cape Town. It became the type specimen of a species named Proterosuchus fergusi in his honour.