J. Stuart Thomson was educated at the University of Edinburgh and then at Freiburg, Germany. He lectured on scientific subjects at various provincial colleges in the United Kingdom and conducted research, particularly in marine zoology. In 1902 he became a member of the British Association for the Advancement of Science and was associated with the Marine Biological Laboratory at Plymouth. By 1906 he was a Fellow of both the Linnean Society and the Royal Society of Edinburgh.
Thomson came to the Cape Colony to fill the post of assistant government biologist, under J.D.F. Gilchrist*. In 1905 he was in addition appointed as a temporary assistant in zoology at the South African College, following the departure of Professor A. Dendy*. From the beginning of 1906 he was an assistant to Gilchrist at the College, as the latter had been appointed acting professor of zoology. This arrangement lasted until October 1907. Meanwhile Thomson had become a member of the South African Association for the Advancement of Science and in December 1906 received a grant from the Association to support his research on South African Alcyonaria (an order of coral polyps of the class Anthozoa). In 1907 he donated a number of books to the College library and left the Cape Colony for Switzerland, where he continued his research under Professor Studer of the University of Bern. His collection of Alcyonaria, which he took with him, contained several genera and a number of species new to science. He studied their anatomy, revised the taxonomy of the order, and wrote up his findings in the form of a doctoral dissertation entitled Alcyonaria of the Cape of Good Hope and Natal (Bern, 1909). The dissertation was published also in the Transactions of the Royal Society of Edinburgh in 1910 (40p).
Thomson continued his research on South African corals in the zoological laboratory of the University of Manchester and during the next few years published three relevant papers in the Memoirs of the Manchester Literary and Philosophical Society: "The Pennatulaceae of the Cape of Good Hope and Natal" (1914-1915, 26p), "South African Gorgonaceae" (1916-1917, 56p), and "The occurrence of Cavernularia Lutkenii K?ll. in the seas of Natal" (1918). Subsequently he published two papers on "South African Alcyonaceae" in the Transactions of the Royal Society of South Africa (1921, Vol. 9, pp. 149-177 and 1924, Vol. 11, pp. 45-85). Other publications by him included papers on "Gorgonaceae" (1911), "Observations on living Gorgonias (Gorgonia verrucosa) occurring in the English Channel" (1912), and "The anatomy of the tortoise" (1932), as well as a book on The animal kingdom (London, 1923). During his younger days he published a poem entitled Eulaline (New York, 1899, 9p).