James Paul Johnson, son of James Johnson and his wife Louisa Catherine, born French, was educated at Dulwich College, London, and then studied at the Royal School of Mines in the same city. Afterwards he gained some practical experience at the Dolcoath and Tincroft Mines in Cornwall. He had a strong interest in geology and stone age archaeology and during 1899-1902 contributed eight geological and archaeological papers, three of them on the Eocene and Pleistocene fauna of Essex, to the Essex Naturalist. In 1902, at the end of the Anglo-Boer War (1899-1902), he came to South Africa, mainly for health reasons. As a certificated mine surveyor he worked at several gold mines on the Witwatersrand, and at the Roberts-Victor diamond mine in the Boshof district of the Orange River Colony (now the Free State). For a brief period he was the mining editor of the South African Mining Journal. Later he practised as a consulting geologist and mining engineer in Johannesburg. He was an associate member of the (British) Institution of Mining and Metallurgy.
Johnson contributed significantly to knowledge of the geology of South Africa. The papers he read before the Geological Society of South Africa, published in its Transactions, dealt with topics such as "Notes on a section through the Witwatersrand beds" (1905), the geology of the Roberts-Victor diamond mine (1907), and the tin, molybdenum and lead occurrences near Potgietersrust (now Mokopane, 1908). His most important contributions to geology were books on The ore deposits of South Africa, with a chapter on hints to prospectors (2 volumes, London, 1908-1909) and The mineral industry of Rhodesia (London, 1911).
Johnson's spare time was devoted to the study of stone tools and the deposits containing them, and in the Transvaal Colony he was one of the pioneers in this field. His work led to the publication of many papers, several of them in the Transactions of the Geological Society of South Africa. In the first of these, "Notes on sections at Shark River and the Creek, Algoa Bay" (1903), he described raised beach deposits containing numerous shells that were identified by James Crawford*. That same year he described his discovery of artefact-bearing deposits near Johannesburg. Later papers dealt with his artefact finds at the confluence of the Taaibosspruit and the Vaal River, south-west of Vereeniging (1904); the farms Vlakfontein 155 (1905) and Waterval 417 (1905); the Krugersdorp Valley (1905); Bulawayo and the Victoria Falls (1905); the Vaal River gravels (with R.B. Young*, 1906); and in a lacustrine deposit near Robinson (1910). His description of the deposits with which many of the artefacts were associated provided useful insights. Meanwhile he had also read a paper on his finds near Johannesburg at the 1904 congress of the South African Association for the Advancement of Science, including a bibliography of the prehistory of South Africa up to that time. When the association met jointly with its British counterpart in Cape Town and Johannesburg the next year he contributed a summary of recent discoveries of stone artefacts in South Africa (many by himself), which was included in the Addresses and papers... published after the meeting. A review paper, "Contribution to our knowledge of the stone age of South Africa", followed the next year, but his main efforts to pull various finds together were published in three small books: The stone implements of South Africa (London, 1907), The prehistoric period in South Africa (London, 1910), and Geological and archaeological notes on Orangia (London, 1910). The latter dealt with the region between the Vaal and Orange rivers. Early in 1906 he donated a collection of geological specimens to the geological museum in Johannesburg. The collection had to be transported to South Africa, presumably from Britain. The next year he was appointed a member of the Bushman Paintings Commission and participated actively in its work.
Johnson was a member of the South African Association for the Advancement of Science (from 1903), the South African Philosophical Society (from 1903), the Geological Society of South Africa, and the Chemical, Metallurgical and Mining Society of South Africa (from 1903). He was a somewhat retiring and reticent person, but to close friends revealed a cheery nature and keen sense of humour. He was interested in science for its own sake and in its pursuit showed indifference to material posessions and comforts. In 1907 he left for Tasmania, where he intended to settle. The files of the Pitt Rivers Museum, Oxford, indicate that he collected a stone tool at Bondi Bay, New South Wales, in 1913. However, he returned to South Africa in 1914, shortly after the outbreak of World War I (1914-1918). While practising as a mine surveyor he died in the influenza epidemic of 1918, aged only 38 years. Unfortunately what remained of his archaeological collection was dispersed after his death. Some of the Later Stone Age artefacts he collected at Taaibosspruit ended up in the Pitt Rivers Museum.
Johnson was married to Annie Maria Wood in Johannesburg in February 1905, but they had no surviving children. After her death he married the widow Millicent Maud Harris in Johannesburg in 1910.