Jan Willem Boudewijn Gunning, the son of a professor of theology, was educated in the Netherlands at the Universities of Amsterdam and Leiden. During his student days he showed an interest in natural history, particularly entomology and ornithology. By 1883 he was practising medicine in the Stellenbosch district, but in that year returned to Europe and in 1884 was awarded the degree Doctor of Medicine (MD) at Jena, Germany. (His highest academic qualification is often wrongly given as PhD). Returning to the Cape he married Suzanna Neethling of Stellenbosch in November that same year. He practised in the Venterstad district (Cape Colony), then in the Free State at Bethulie and Smithfield, and finally at Edenburg. After his wife died in 1888 he married Miss Ellen E. Dobbin of Bethulie in November 1889. In 1896 he moved to Pretoria where he was appointed as an assistant at the State Museum (later the Transvaal Museum, now the Ditsong National Museum of Natural History) in October. In April 1897 he became acting director, and in December of that same year the museum's first permanent director. He also taught zoology at the State Gymnasium (a high school) in Pretoria.
The museum grew rapidly under his directorship. C.J. Swierstra* soon joined the staff as entomological assistant, followed by Miss R. Leendertz* as botanical assistant and, in 1906, Dr L.H. Gough* as assistant for lower vertebrates and invertebrates except insects. Gunning himself acted as keeper of the mammalian and ornithlogical collections. Live animals acquired by him formed the nucleus of the Transvaal Zoological Gardens, which developed into Pretoria's National Zoological Gardens. The animals were moved to the present site of the Zoo, on the farm Rus in Urbe just north of central Pretoria, in 1899. A new museum building in Boom Street was started in 1899 and the museum moved into it in 1902, at the end of the Anglo-Boer War (1899-1902), after Gunning had been re-appointed by the British authorities despite his pro-Boer sympathies. He was a hard and enthusiastic worker with a kind and cheerful disposition. His strenuous efforts to enlarge the collections, coupled with the administration of both the museum and zoological gardens, left him little time for research. By 1908 the museum had extensive zoological collections, an herbarium, and collections of mineralogical, palaeontological, historical and ethnographical specimens and coins, and the zoological gardens were well developed. In April 1908 the first number of the Annals of the Transvaal Museum was published, to which Gunning contributed "A short history of the Transvaal Museum" (pp. 1-13). He later also contributed notes on some scarce South African coins minted in Griquastad (in Dutch, 1910, Vol. 2(3), pp. 170-172). In 1909 he undertook a tour of major museums in the Netherlands and Germany.
Gunning's research related mainly to ornithology. He was one of the founders of the South African Ornithologists' Union in April 1904, served on its editorial committee from 1906 to 1913, held the office of joint vice-president from 1904 to 1909, and that of president from 1910 to his death in 1913. He contributed two papers to its Journal: "On a new genus and species belonging to the Fringillidae from the Transvaal" (1907, Vol. 3(2), pp. 208-210) and "On the South African species of Centropus" (with A.K. Haagner*, 1908, Vol. 4(1), pp. 36-37). A paper by him on "Locust birds" was published in the Transvaal Agricultural Journal (1907/8, Vol. 6, pp. 527-). Several further papers relating to ornithology appeared in the Annals of the Transvaal Museum: A description of two new species of birds in the museum's collections (1909, Vol. 1, pp. 173-174); "A check list of the birds of South Africa", with A.K. Haagner (a list of 920 species known to occur south of the Zambesi-Cunene line; 1910, Supplement to Vol. 2, pp. 71-156); a list of the museum's collection of birds' eggs (1911, Vol. 3, pp. 20-28), and, with Austin Roberts*, "New records and descriptions of new species of birds in the Transvaal Museum collection" (1911, Vol. 3, pp. 109-118). The species Sheppardia gunningi (East Coast Akalat) was named in his honour by Haagner in 1909.
Gunning was elected a Fellow of the Zoological Society of London and was a foundation member of the Transvaal Biological Society in 1907, serving as its president in 1910 and again in 1913. In January 1908 he exhibited a diseased skull of a baboon before the society, and in May 1911 read a paper on the re-discovery of Burchell's zebra. His interest in agriculture led him to participate in the founding, in September 1897, of the Vereeniging van Transvaalsche Landbouw Genootschappen (later the Transvaal Agricultural Union), of which he was elected a life vice-president. His service in this role, and contributions to the improvement of agriculture in the Transvaal, led to his being awarded the Chevalier du Merite Agricole (a medal of honour) by the French government in 1905. He was also active in the Pretoria Agricultural Society, the Transvaal Kennel Club, and the Pretoria Homing Society. After being a member of the South African Philosophical Society from 1896 to about 1900, he joined its successor, the Royal Society of South Africa, in 1908. He was also an early member of the South African Association for the Advancement of Science, serving on several of its committees over the years and as a member of council in 1908/9. At the annual meeting in 1908 he read a paper on "Matters concerning museums in South Africa", which was published in the association's Report (pp. 275-283) for that year. He was even a corresponding member of the Philosophical Society of the Orange River Colony.
By 1912 Gunning was in such poor health that he went to Europe to visit hot springs in Germany. During this visit Queen Wilhelmina of the Netherlands made him a Knight of Orange-Nassau. Meanwhile further expansion of the Transvaal Museum had eventually led to the erection of a new and larger museum building in Paul Kruger Street, which was completed in 1913. However, Gunning died from a kidney complaint before the collections were moved to their new home. He was succeeded as director by Dr H.G. Breijer*.