James F. S. Allen, son of William Allen and his wife Clara Delinda Allen, qualified as Doctor of Medicine (MD) and Master of Surgery (MCh) at Queen's University in Cork, Ireland, in 1874. He emigrated to Natal to become a partner of Dr. W.J. Scott in Pietermaritzburg and was licensed to practice in Natal in February 1875, being appointed as additional district surgeon in Pietermaritzburg at the same time. In 1876 he assumed control of Grey's Hospital in Pietermaritzburg as its only surgeon and visiting physician and during the 1880's developed it into one of the foremost medical institutions in the country. He acquired a reputation as a diagnostician and believed that surgery should be used only as a last resort.
Early in 1876 Allen experimented with chloral as an anaesthetic for children, finding that the administration of three to four grams produced unconsciousness for three to four hours. However, it proved unsatisfactory with adults. During 1884-1886 an outbreak of enteric fever in Pietermaritzburg led Allen to compile a report on it entitled Is enteric fever a cattle disease? (Pietermaritzburg, 1885, 59p). He contributed articles on a variety of other medical and health topics to the local press, including one on the natural immunity of people in Natal to tuberculosis, a topic on which he did much research. In 1895 he was elected president of the third congress of the South African Medical Association, held in Durban.
Allen resigned his hospital surgeoncy in 1900 and returned to England, attending the British Tuberculosis Conference in 1901. However, by 1909 he was back in Pietermaritzburg to farm and resume his private practice. That year he published a paper on "Bilharzia haematobia and circumcision" in the Lancet, giving his address as Pietermaritzburg.
Allen was married in Pietermaritzburg in January 1882. He and his wife, Jane C. Allen, had three daughters and two sons. He was a compassionate man and did much for charity, but readily entered into controversy. He had a long feud with his namesake, Dr Richmond Robert Allen, who also practiced in Pietermaritzburg from 1882, about their mail being mixed up and patients mistaking one for the other. Dr R.R. eventually sued Dr J.F.S and after a much publicised trial in 1889 was awarded damages of 15 pounds sterling.