Key questions in paleoneurology concern the timing and emergence of derived cerebral features within the human lineage. Endocasts are replicas of the internal table of the bony braincase that are widely used in paleoneurology as a proxy for reconstructing a timeline for hominin brain evolution in the fossil record. The accurate identification of cerebral sulci imprints in endocasts is critical for assessing the topographic extension and structural organisation of cortical regions in fossil hominins. High-resolution imaging techniques combined with established methods based on population-specific brain atlases offer new opportunities for tracking detailed endocranial characteristics. This study provides the first documentation of sulcal pattern imprints from the superolateral surface of the cerebrum using a population-based atlas technique on extant human endocasts. Human crania from the Pretoria Bone Collection (South Africa) were scanned using micro-CT. Endocasts were virtually extracted, and sulci were automatically detected and manually labelled. A density map method was applied to project all the labels onto an averaged endocast to visualise the mean distribution of each identified sulcal imprint. This method allowed for the visualisation of inter-individual variation of sulcal imprints, for example, frontal lobe sulci, correlating with previous brain-MRI studies and for the first time the extensive overlapping of imprints in historically debated areas of the endocast (e.g. occipital lobe). In providing an innovative, non-invasive, observer-independent method to investigate human endocranial structural organisation, our analytical protocol introduces a promising perspective for future research in paleoneurology and for discussing critical hypotheses on the evolution of cognitive abilities among hominins.