John Alfred Vaughan, mechanical engineer, was the son of Henry Vaughan. He was educated at the City of London School and continued his training at the Royal Naval Engineering College, Devonport, and the Royal Navy College at Greenwich, London. In due course he became a member of the Institution of Mechanical Engineers and the American Society of Mechanical Engineers, and later also of the Institution of Civil Engineers. For 15 years he served as an engineering officer in the Royal Navy, on board HMS Champion, Undaunted, Rainbow, and Monarch, but then retired as a result of ill health. In November 1901 he married Eileen N. Clarke of Simonstown, with whom he had one daughter. In April that same year he was appointed as chief inspector of machinery in the Department of Mines of the Transvaal Colony (and later of the Union of South Africa), and head of the Government Mechanical Testing Laboratory in Johannesburg.
In 1905 Vaughan was en examiner in mechanical and electrical engineering for the second mining examination of the University of the Cape of Good Hope. The government of the Transvaal Colony nominated him as its representative on the council of the Transvaal University College (1906) and on the Rope and Safety Catch Commission. He contributed much to the safety of winding ropes as used in the gold mines and among others published a paper on "Safety in winding operations" (Report of the South African Association for the Advancement of Science, 1918, pp. 205-216). Later he presented a paper, "Notes on deep-level mining", at the Empire Mining and Metallurgical Congress in London. The paper was published in the Journal of the South African Institution of Engineers (1924, 32p). Six years later he edited the Proceedings of the Empire Mining and Metallurgical Congress (Johannesburg, 1930).
Vaughan was a member of the Mechanical Engineers' Association of the Witwatersrand, which changed its name in 1905 to the Transvaal Institute of Mechanical Engineers. With W.M. Epton as co-author he contributed an important paper on "Wire ropes used for winding: their strength and some causes of its reduction", for which they were awarded the institute's gold medal in 1905. Vaughan served on the institute's council from 1905 or earlier, and as honorary secretary during 1907-1910. He was elected president for 1910/1. During his presidency the institute amalgamated with the South African Association of Engineers (of which he was also a member, and a former vice-president) to form the South African Institution of Engineers, of which he automatically became the first president. By 1913 he served as chairman of the editorial committee that published the institution's Transactions, and in 1918/9 was the joint winner (with H.S. Potter) of the institution's gold medal for his contributions to the safety of wire ropes used for winding. He joined the South African Association for the Advancement of Science in 1903.
Vaughan retired as chief inspector of machinery around 1925 and for some time practised as a consulting engineer.