John G. Baker was educated at Quaker schools and showed an interest in natural history from an early age. When he was 15 he began writing botanical articles, and later impressed botanists with his review of the indigenous roses of Britain. In 1866 he was appointed assistant in the library at the Royal Botanical Gardens at Kew and two years later, as co-author with W.J. Hooker, took part in writing Synopsis filicum; or, a synopsis of all known ferns... (London, 1868, 482p). He was eventually promoted to keeper of the herbarium and gardens in 1890 and also lectured in botany at the London Hospital Medical School. Though he retired as keeper in 1899 he continued to lecture in botany to the gardeners at Kew for some years, and continued his research at the herbarium there to 1917. He published many books and numerous articles, particularly on the systematics of plants, and was considered an authority on ferns, roses, monocotyledons, and some dicotyledon families. His more important publications included "Contributions to the flora of Madagascar" (Journal of the Linnean Society (Botany), 1883, 217p), Flora of Mauritius and the Sychelles... (London, 1877, 557p), and Flora of the English Lake District (London, 1885). Three genera and a number of species were named in his honour.
Baker was a member of the Royal Irish Academy, a fellow of the Royal Society and of the Linnean Society, and in 1889-1991 and 1893-1894 acted as vice-president of the latter. An honorary D.Sc. degree was bestowed upon him by the University of Leeds in 1919.
Baker did not visit South Africa. His contributions to the botany of southern Africa included a number of important papers in the Journal of the Linnaean Society which dealt with plants of the region, including the Scilleae and Chlorogaleae (1873), Asparagaceae (1875), Anthericeae and Eriospermeae (1876), Iridaceae (1877), Hypoxidaceae (1878), and Aloineae and Yuccoideae (1880), as well as his Handbook of the fern-allies (London, 1887), Handbook of the Amaryllideae... (London, 1888) and Handbook of the Irideae (London, 1892). Hence in 1895 Rudolph Marloth* could remark in his review of South African science that "The Liliaceae, Iridaceae, Amaryllidaceae, and allied orders, were sufficiently dealt with in Mr. Baker's general monographs...". Baker's descriptions of 1400 species of Cape bulbs furthermore comprised the whole Volume 6 of the Flora Capensis, published in 1896-7. He also described a number of new South African species in various articles. One of his papers, "The genus Albuca in the herbarium of the Albany Museum" was published in South Africa, in the Records of the Albany Museum, 1903-1906, Vol. 1, pp. 89-95.
Baker was the father of the botanist Edmond Gilbert Baker*.