The origin and evolution of hominin mortuary practices are topics of intense interest and debate. Human burials dated to the Middle Stone Age (MSA) are exceedingly rare in Africa and unknown in East Africa. Here, we describe the partial skeleton of a c. 2.5-3.0 year-old child dating to 78.3 ± 4.1 ka, recovered in the MSA layers of Panga ya Saidi (PYS), a cave site in the tropical upland coast of Kenya. Recent excavations revealed a pit feature containing a child in a flexed position. Geochemical, granulometric and micromorphological analyses of the burial pit content and encasing archaeological layers indicate that the feature was deliberatly excavated. Taphonomical evidence such as the strict articulation or good anatomical association of the skeletal elements and histological evidence of putrefaction support the in-place decomposition of a fresh body. Absent to minimal displacement of the unstable joints during decomposition points to an interment in a filled space (grave earth) making the PYS finding the oldest human burial in Africa. The morphological assessment of the partial skeleton is consistent with its assignment to H. sapiens, although the preservation of some primitive features in the dentition supports increasing evidence for non-gradual accretion of modern traits during the emergence of our species. The PYS burial sheds new light on how MSA populations interacted with the dead.