PurposeTo evaluate the corneal epithelial thickness by anterior segment OCT in children with vernal keratoconjunctivitis (VKC) compared to normal participants.Patient and methodsA cross-sectional case control observational study was conducted on children aged from 5 to 18 years with VKC. The study included 142 eyes divided into two groups: 71 eyes of VKC group and 71 eyes of age matched control group. Anterior segment OCT epithelial mapping for the central 5-mm was done to evaluate epithelial thickness-based variables.ResultsCorneal epithelial thickness mapping showed significant superior thinning (51.07 ± 4.11) μm in VKC group compared to controls (52.54 ± 2.01) μm (p= 0.008), a decreased MIN epithelial thickness (45.99 ± 6.52) μm compared to controls (50.11 ± 1.91) μm (p< 0.001) and more negative (MIN–MAX) value (− 11.77 ± 9.38) indicating focal epithelial thinning compared to (− 5.80 ± 1.88) in controls (p= 0.001). In palpebral VKC, MIN epithelial thickness showed significant thinning (48. 38 ± 3.45) μm compared to controls (50.11 ± 1.91) μm (p= 0.001). Eyes with mixed VKC showed superior epithelial thinning (50.70 ± 4.59) μm compared to (52.54 ± 2.01) μm in controls (p= 0.025) and significant decreased MIN epithelial thickness (43.78 ± 7.83) μm compared to (50.11 ± 1.91) μm in control group.ConclusionsVKC is a disease primarily affecting the corneal epithelium. Corneal epithelial thickness mapping may be considered to assess the integrity of the ocular surface in eyes with VKC, and to detect corneal epithelial changes. Disease phenotype may influence the corneal epithelial changes, and the disease duration is another factor influencing these changes.