As a girl, Mary exhibited a natural talent for drawing and was interested in archaeology. After undergoing sporadic schooling, she participated in excavations of a Neolithic Period site at Hembury, Devon, England, by which time she had become skilled at making reproduction-quality drawings of stone tools. She met Louis Leakey in 1933, and they were married in 1936. Shortly thereafter they left for an expedition to East Africa, an area that became the central location of their work.

Working alongside Louis Leakey for the next 30 years, Mary Leakey oversaw the excavation of various prehistoric sites in Kenya. Her skill at the painstaking work of excavation surpassed her husband's, whose brilliance lay in interpreting and publicizing the fossils that they uncovered. In 1948, on Rusinga Island in Lake Victoria, she discovered the skull of Proconsul africanus, an ancestor of both apes and early humans that lived about 25 million years ago. In 1959 at Olduvai Gorge, Tanzania, she discovered the skull of an early hominin (member of the human lineage) that her husband named Zinjanthropus, or “eastern man,” though it is now regarded as Paranthropus, a type of australopith (Australopithecus), or “southern ape.”

After her husband's death in 1972, Leakey continued her work in Africa. In 1978 she discovered at Laetoli, a site south of Olduvai Gorge, several sets of footprints made in volcanic ash by early hominins that lived about 3.5 million years ago. The footprints indicated that their makers walked upright; this discovery pushed back the advent of human bipedalism to a date earlier than the scientific community had previously suspected. Among Mary Leakey's books were Olduvai Gorge: My Search for Early Man (1979) and the autobiographical Disclosing the Past (1984).