The reported incidence of neoplasia in the extinct hominin record is rare. We describe here the first palaeopathological analysis of an osteogenic lesion in the extinct hominin Homo naledi from Dinaledi Cave (Rising Star), South Africa. The lesion presented as an irregular bony growth, found on the right lingual surface of the body of the adult mandible U.W. 101-1142. The growth was macroscopically evaluated and internally imaged using micro-focus x-ray computed tomography (μCT). A detailed description and differential diagnosis were undertaken using gross and micromorphology, and we conclude that the most probable diagnosis is peripheral osteoma – a benign osteogenic neoplasia. These tumours are cryptic in clinical expression, though they may present localised discomfort and swelling. It has been suggested that muscle traction may play a role in the development and expression of these tumours. The impact of this lesion on the individual affected is unknown. This study adds to the growing corpus of palaeopathological data from the South African fossil record, which suggests that the incidence of neoplastic disease in deep prehistory was more prevalent than traditionally accepted. The study also highlights the utility of micro-computed tomography in assisting accurate diagnoses of ancient pathologies.