Born in Moscow, he studied medicine at Dorpat (now called University of Tartu), Göttingen, Berlin and Prague, but did not practise for long. After a series of short journeys to Iceland (1869), Western Africa (1873), Tunis (1874) and Lower Egypt (1875), he remained almost continuously in eastern Equatorial Africa from 1875 to 1886, making first Khartoum and afterwards Lado the base of his expeditions.
Junker was a leisurely traveller and a careful observer; his main object was to study the peoples with whom he came into contact, and to collect specimens of plants and animals, and the result of his investigations in these particulars is given in his Reisen in Afrika (3 vols., Vienna, 1889–1891), a work of high merit. An English translation by A. H. Keane was published in 1890-1892.
He investigated the Nile-Congo watershed, successfully combated Georg Schweinfurth's hydrographical theories, and established the identity of the Welle and Ubangi rivers. The Mahdist rising prevented his return to Europe through the Sudan, as he had planned to do, in 1884, and an expedition, fitted out in 1885 by his brother in St Petersburg, failed to reach him. Junker then determined to go south. Leaving Wadelai on 2 January 1886 he travelled by way of Uganda and Tabora and reached Zanzibar in November 1886. In 1887 he received the gold medal of the Royal Geographical Society. As an explorer Junker is entitled to high rank, his ethnographical observations in the Niam-Niam (Azande) country being especially valuable although unsubstantiated in parts. He died at St. Petersburg.
See the biographical notice by E. G. Ravenstein in Proceedings of the Royal Geographical Society (1892), pp. 185–187.
- Travels in Africa: During the years 1875-1878: Volume 1 (1890)
- Travels in Africa: During the years 1879-1883: Volume 2 (1891)
- Travels in Africa during the years 1882-1886: Volume 3 (1892)
- Robert Brown (1893) The story of Africa and its explorers, Cassell & Co., London 
- "Review: Travels in Africa, 1882–1886". The Saturday Review of Politics, Literature, Science and Art. 74: 570. November 12, 1892.
- This article incorporates text from a publication now in the public domain: Chisholm, Hugh, ed. (1911). "Junker, Wilhelm". Encyclopædia Britannica (11th ed.). Cambridge University Press.
- Rines, George Edwin, ed. (1920). "Junker, Wilhelm". Encyclopedia Americana.