The son of a merchant, Baker lived on the Indian Ocean island of Mauritius (1843–45) and in Ceylon (1846–55) before traveling through the Middle East (1856–60). In 1861, with Florence von Sass (who later became his second wife), he went to Africa and for about a year explored the Nile tributaries around the Sudan and Ethiopia border. Using maps supplied by Speke, the Baker expedition set out in February 1863 to find the source of the Nile. In March 1864 Baker determined the source to be a lake, which he named Albert Nyanza (Albert, Lake) (Lake Albert), lying between modern Uganda and Congo (Kinshasa). He was knighted in 1866, the year after he returned to England.

In 1869 the Ottoman viceroy of Egypt, Ismāʿīl Pasha, asked Baker to command a military expedition to the Nile equatorial regions. There the explorer helped to put down the slave trade and annexed territories of which he was appointed governor general for four years. His books include The Rifle and the Hound in Ceylon (1854) and The Nile Tributaries of Abyssinia (1867).