Bilateral coronal synostosis causes functional and morphological problems that require fronto-orbital advancement in infancy to correct the brachycephalic deformity and to prevent mental impairment caused by the intracranial hypertension. In this study, 99 children with isolated cases of brachycephaly were prospectively followed to study their preoperative and postoperative mental outcome, which was evaluated using developmental or intelligence quotients. Several factors were analyzed: age before treatment, age at the time of surgery, and the correlation between mental assessments before and after surgery. In a subgroup or patients tested for the FGFR3 P250R mutation (n = 48), mental and morphological assessments were analyzed. Before surgery, mental status was better in the patients tested before 1 year of age (p < 0.001). The preoperative mental assessment always correlated with the postoperative assessment (p < 0.0001). The postoperative mental outcome was better when surgery was performed before the patient reached 1 year of age (p < 0.02). Although both the morphological and functional outcomes were better in the subgroup of noncarriers of the mutation, the differences were not statistically significant. Prominent bulging of the temporal fossae was frequently responsible for poor morphological outcome in carriers of the mutation. This study confirms the need for early corrective surgery before 1 year of age in brachycephalic patients to prevent impairment of their mental development. Suboptimal morphological and mental outcomes can be expected in patients with nonsyndromic brachycephaly who carry the FGFR3 P250R mutation. Primary correction of the temporal bulging should be performed in conjunction with fronto-orbital advancement to improve the morphological outcome in patients with the mutation.