Humans show a unique pattern of brain growth that differentiates us from all other primates. In this study, we use virtual endocasts to provide a detailed description of shape changes during human postnatal ontogeny with geometric morphometric methods. Using CT scans of 108 dried human crania ranging in age from newborns to adults and several hundred landmarks and semi-landmarks, we find that the endocranial ontogenetic trajectory is curvilinear with two bends, separating three distinct phases of shape change. We test to what extent endocranial shape change is driven by size increase and whether the curved ontogenetic trajectory can be explained by a simple model of modular development of the endocranial base and the endocranial vault. The hypothesis that endocranial shape change is driven exclusively by brain growth is not supported; we find changes in endocranial shape after adult size has been attained and that the transition from high rates to low rates of size increase does not correspond to one of the shape trajectory bends. The ontogenetic trajectory of the endocranial vault analyzed separately is nearly linear; the trajectory of the endocranial base, in contrast, is curved. The endocranial vault therefore acts as one developmental module during human postnatal ontogeny. Our data suggest that the cranial base comprises several submodules that follow their own temporally and/or spatially disjunct growth trajectories.