Hominin fossils from the African mid-Pleistocene are rare despite abundant Acheulean tools in Africa and apparently African-derived hominins in Eurasia between 1.0 and 0.5 million years ago (Ma). Here we describe an African fossil cranium constrained by 40Ar/39Ar analyses, magnetostratigraphy, and sedimentary features to 0.97 to 0.90 Ma, and stratigraphically associated with Acheulean handaxes. Although the cranium represents possibly the smallest adult or near-adult known between 1.7 and 0.5 Ma, it retains features observed in larger Homo erectus individuals, yet shows a distinct suite of traits indicative of wide population variation in the hominins of this period.