Ametropia is reported as a common ophthalmic manifestation in craniosynostosis. We retrospectively compared childhood refractive error and ocular biometric features of fibroblast growth factor receptor (FGFR)-related syndromic craniosynostosis patients with those of non-syndromic craniosynostosis and control subjects. Thirty-six eyes (18 patients) with FGFR-related syndromic craniosynostosis, 76 eyes (38 patients) with non-syndromic craniosynostosis, and 114 eyes (57 patients) of intermittent exotropes were included in the analysis. Mean age at examination was 7.82 ± 2.51 (range, 4–16) years and mean spherical equivalent was -0.09 ± 1.46 Diopter. Mean age and refractive error were not different between groups, but syndromic craniosynostosis patients had significantly longer axial length, lower corneal power, and lower lens power than other groups (p < 0.01, p < 0.01, and p < 0.01, respectively). Axial length was positively correlated and keratometry and lens power were negatively correlated with age in non-syndromic craniosynostosis and controls, while these correlations between age and ocular biometric parameters were not present in the FGFR-related syndromic craniosynostosis. In conclusion, ocular biometric parameters in FGFR-related syndromic craniosynostosis differed from those of non-syndromic craniosynostosis and age-matched controls, and did not show the relations with age, suggesting this cohort may have abnormal refractive growth.