Leakey was educated at the Duke of York School in Lang'ata with his two younger brothers. After leaving school Leakey often accompanied his parents to dig sites, frequently wandering about on his own in search of fossils. On 4 November 1960, Leakey discovered the OH 7 fossils at Olduvai Gorge, Tanzania. The bones, nicknamed "Johnny's Child", were (along with other hominid fossil fragments found earlier by his parents) formerly described as a new species in the genus Homo in April 1964. OH 7 is now considered the type specimen of Homo habilis.
Leakey did not follow his parents' profession and has never been particularly active within the field of palaeoanthropology; however, his younger brother, Richard, is a noted paleoanthropologist and conservationist. Leakey now operates the Nakuru-based company Jonathan Leakey Ltd., which supplies East African snake venoms and medicinal plants for antivenom manufacturers, medical research facilities, and pharmaceutical companies.