Key questions in paleoneurology concern the timing and emergence of derived cerebral features of modern humans. Endocasts (i.e., a replica of the internal table of the bony brain case) constitute a proxy for reconstructing a timeline for hominin brain evolution in the fossil record. The identification of cerebral imprints is critical for assessing the topographic extension and structural organisation of cortical areas, however, describing these crucial landmarks in fossil endocasts is challenging due to the fragmentary nature of fossil specimens. The application of high-resolution imaging techniques combined with established methods used in population specific brain atlases offers new opportunities for tracking detailed endocranial cerebral characteristics. In this context, our study aims to provide an atlas that documents variation in extant human endocranial sulcal patterns for subsequent use as a comparative platform for the study of the fossil record. Dry human crania from the Pretoria Bone Collection were scanned using micro-CT at Necsa, Pelindaba (South Africa). Endocasts were virtually extracted and sulci were detected using freely available automatic techniques. Using a customized open source MATLAB script we manually labelled the sulci that could be identified. Finally, a density map method was applied to project all the labels onto an averaged endocast and to visualise the mean distribution of each identified sulcal imprint. In providing an innovative, non-invasive, observer-independent method to investigate human endocranial structural organisation, our analytical protocol introduces a promising perspective for future endocranial research in paleoneurology and for discussing well-founded hypotheses on the evolution of cognitive abilities among hominins.