In a continuation of a prospective longitudinal cohort study in a healthy population on the course of skull shape from birth to 24 months, at 5 years of age, 248 children participated in a follow-up assessment using plagiocephalometry (ODDI—oblique diameter difference index, CPI—cranio proportional index). Data from the original study sampled at birth, 7 weeks, 6, 12, and 24 months were used in two linear mixed models. Main findings: (1) if deformational plagiocephaly (ODDI <104%) and/or positional preference at 7 weeks of age are absent, normal skull shape can be predicted at 5 years of age; (2) if positional preference occurs, ODDI is the highest at 7 weeks and decreases to a stable lowest value at 2 and 5 years of age; and (3) regarding brachycephaly, all children showed the highest CPI at 6 months of age with a gradual decrease over time. Conclusion: The course of skull deformation is favourable in most of the children in The Netherlands; at 5 years of age, brachycephaly is within the normal range for all children, whereas the severity of plagiocephaly is within the normal range in 80%, within the mild range in 19%, and within the moderate/severe range in 1%. Medical consumption may be reduced by providing early tailored counselling.