In 1847 St John's father, the journalist James Augustus St. John, introduced him to James Brooke. He went out to Sarawak the following year to become Brooke's private secretary and thus began his diplomatic career. He was British Consul General in Brunei from 1856 and in 1858 made two ascents of Mount Kinabalu with Hugh Low. One of the peaks of Mount Kinabalu, "St John's Peak" (4,091 m – 4 metres shorter than the summit, "Low's Peak"), is named in his honour. He wrote a book about his explorations in Borneo, Life in the Forests of the Far East (1862), and two biographies of James Brooke (1879 and 1899).
In 1863 St John became British chargé d'affairesinHaiti and in 1871 took up the same post in the Dominican Republic. He was promoted to Minister in Haiti late in 1872, and was chargé d'affaires in Lima and Minister in Peru from 1874 to 1883, during which time he was awarded the KCMG. While in Peru he made a collection of pottery which is now in the British Museum.[3]
In 1884 St John published a memoir of his experiences in Haiti, Hayti: Or, The Black Republic, which caused public outrage with its sensational tales of cannibalism in the Vodou religion. He is also quoted as saying that "The History of the country [Haiti] ... is but a series of plots and revolutions followed by barbarous military executions."
St John had a relationship with a Malay woman named Dayang Kamariah, with whom he had a son, Sulong, later baptised as Charles when he was 10. He later trained as a civil engineer, and worked in a government position in Perak.[5]
In 1899, at the age of 73, he married the 31-year old Mary Armstrong in Paris. They settled in Camberley, and he died on 3 January 1910.[6]