Background: In recent years the Later Stone Age has been redated to a much deeper time depth than previously thought. At the same time, human remains from this time period are scarce in Africa, and even rarer in West Africa. The Iwo Eleru burial is one of the few human skeletal remains associated with Later Stone Age artifacts in that region with a proposed Pleistocene date. We undertook a morphometric reanalysis of this cranium in order to better assess its affinities. We also conducted Uranium-series dating to re-evaluate its chronology. Methodology/Principal Findings: A 3-D geometric morphometric analysis of cranial landmarks and semilandmarks was conducted using a large comparative fossil and modern human sample. The measurements were collected in the form of three dimensional coordinates and processed using Generalized Procrustes Analysis. Principal components, canonical variates, Mahalanobis D2 and Procrustes distance analyses were performed. The results were further visualized by comparing specimen and mean configurations. Results point to a morphological similarity with late archaic African specimens dating to the Late Pleistocene. A long bone cortical fragment was made available for U-series analysis in order to re-date the specimen. The results (~11.7-6.3 ka) support a terminal Pleistocene chronology for the Iwo Eleru burial as was also suggested by the original radiocarbon dating results and by stratigraphic evidence. Conclusions/Significance: Our findings are in accordance with suggestions of deep population substructure in Africa and a complex evolutionary process for the origin of modern humans. They further highlight the dearth of hominin finds from West Africa, and underscore our real lack of knowledge of human evolution in that region. Copyright 2011 Harvati et al.