Morphological correction is one of the main aims of surgery for sagittal synostosis (SSO). Different surgical techniques have been developed; however, few studies have compared the different surgical protocols. The morphological outcome is poorly documented, because a consensual evaluation tool is lacking. We performed a prospective study of children operated for SSO in our institution. Children were operated whenever possible at 4 months for craniectomy; by default, children underwent cranioplasty at or after 9 months. The morphological outcome of all children was evaluated using traditional craniometry with head circumference (HC) and the cephalic index (CI), and with the Rotterdam scaphocephaly morphology score (RSMS), a total of semi-quantitative assessments of morphological hallmarks. Craniectomy was significantly associated with a shorter operation time and hospital stay, and a better impact on HC and CI measurements, compared with cranioplasty. The RSMS was markedly improved after surgery in both groups; however, we found no significant difference in improvement between the two groups. Although the transfusion rate and the prevalence of developmental delay were lower in the craniectomy group, and reoperations for calvarial lacunae or complex craniosynostosis occurred only this group, these differences were not significant. Our results support early surgery with craniectomy whenever possible; however, cranioplasty at a later age is a very acceptable by-default indication. In addition to classical craniometry, morphological evaluation using the RSMS or a similar quantitative scale appears highly desirable for future studies.