Apert syndrome is mostly caused by one of the two specific point mutations in the fibroblast growth factor receptor 2 (FGFR2). The objective of this study was to determine whether there were any differences in the prevalence of ophthalmic features in Apert syndrome when comparing the Ser252Trp and Pro253Arg mutations in FGFR2. This was a retrospective study of patients with Apert syndrome with genotype analysis. The prevalence of five ophthalmic features, visual impairment, amblyopia, strabismus, corneal abnormality, and pale optic discs, were compared between the two FGFR2 genotypes. There were 25 (74%) cases with Ser252Trp mutation, and 9 (26%) cases with the Pro253Arg mutation in FGFR2. Ophthalmic findings in 20 cases of FGFR2 Ser252Trp and 9 cases of Pro253Arg mutation were compared. Visual acuity worse than 6/12 in at least one eye was present in 60% patients with FGFR2 Ser252Trp mutation compared with 12.5% patients with Pro253Arg mutation (P < 0.05). Forty percent of eyes with FGFR2 Ser252Trp mutation compared with 12.5% eyes with Pro253Arg mutation were worse than 6/12. There was a trend of more frequent amblyopia and strabismus in FGFR2 Ser252Trp mutation and more frequent optic disc pallor in the FGFR2 Pro253Arg mutation. There was a differential effect of FGFR2 mutations in ophthalmic findings in patients with Apert syndrome, with significantly greater prevalence of visual impairment in the Ser252Trp mutation compared with the Pro253Arg mutation. Further study would elucidate whether the trends in differential effects between the two mutations in amblyopia, strabismus, and optic disc pallor represent real differences.