Purpose: To observe whether the effect of orthokeratology (OK) lenses on myopia control in children with allergic conjunctivitis (AC) after three years of wear differs from that in children without allergic conjunctivitis (nAC) and to identify potential influencing factors. Methods: This was a retrospective case‒control study. Patients aged 8-15 years who were fitted with OK lenses in 2019 and had a spherical equivalent (SE) between -6 and -0.75 dioptres and astigmatism ≥-1.50 D were collected. A three-year follow-up was also conducted, documenting all corneal adverse events (AEs) and the increase in axial length (AL) of the eye after three years of wearing OK lenses. Patients were divided into groups with and without AC based on their medical history and physical signs at the initial fitting. Only the right eye data of patients were used for statistical analysis. Baseline data and AL elongation after three years were compared between the two groups. Results: A total of 309 patients were included in this study, with 47 in the AC group and 262 in the nAC group. There were no statistically significant differences between the two groups in terms of age , sex, SE, AL of the eye and environment. During the three-year follow-up period, 20 patients (42.6%) in the AC group and 75 patients (28.6%) in the nAC group experienced AEs, and these two groups were not significantly different ( P=0.057). After three years of OK lens wear, the AL elongation in the AC group was 0.96±0.45 mm, whereas it was 0.69±0.45 mm in the nAC group (P<0.001). The AL elongation in AC patients was significantly greater than that in nAC patients. AL elongation was not correlated with the occurrence of AEs. In the AC group, AL elongation was correlated only with age, while in the nAC group, axial elongation was related to age, initial SE, and initial AL. Conclusions: In children with AC, the effect of wearing OK lenses on controlling axial elongation is weaker than that in patients without AC. This attenuation is unrelated to the occurrence of corneal AEs.