The evolutionary diversity across the genus Homo encompasses variation in brain size and overall brain shape. Homo naledi, from the Rising Star cave system of South Africa, is near the extreme of small brain size within Homo but is easily recognized as Homo in other aspects of endocast morphology. Previous work on the endocast of H. naledi has focused on cranial fossils from the Dinaledi Chamber. Here we add evidence of the endocast morphology of Homo naledi with the LES1 cranium from the Lesedi Chamber. This is the most complete representation of endocranial morphology yet known for H. naledi and confirms the anatomical form from more fragmentary material from the Dinaledi Chamber. Global endocast measurements show a posteriorly wide shape in H. naledi relative to endocranial volume. Qualitative description and metric comparisons show that LES1 and the DH3 endocast have derived morphology relative to chimpanzees and australopiths of the posterolateral frontal lobe and posterior occipital/parietal region. These traits are shared with Homo sapiens and endocasts of later Homo erectus and Neandertals. The orbital cap morphology may reflect a common ancestry of H. naledi with these groups, or parallelism between this smaller-brained lineage and species with larger brain sizes.