Introduction Refractive error is one of the most common causes of visual impairment in the world, negatively affecting a patient's quality of life, economic opportunities and more. Although numerous studies have explored the impact of severe ocular allergies on refractive error, there is limited research on how relatively mild forms of ocular allergies may affect vision. This study aims to assess the impact of allergic conjunctivitis, a milder and more common ocular allergy, on the development and progression of refractive error in the pediatric population. Methods This was a retrospective study that reviewed the records (2015-2018) of 198 established pediatric patients from the Ross Eye Institute: 90 with a new diagnosis of allergic conjunctivitis, and 108 age- and sex-matched controls. All refractions were performed by a single board-certified and fellowship-trained pediatric ophthalmologist utilizing retinoscopy, the gold standard for measuring refractive error in the pediatric population. T-tests were used to analyze continuous variables, and chi-square tests were used for categorical variables. Linear regression was used to identify factors associated with refractive error. Results The average age of the patient population was 9.7 years, with 42% males. Children with allergic conjunctivitis were found to have a significantly higher incidence of cylindrical refractive error compared to controls (56% vs 34%, p < 0.001), with increased cylindrical power (1.20 ± 0.07 D vs 0.80 ± 0.08 D; p < 0.001), but no difference in spherical equivalent (-0.83 ± 0.27 vs -0.66 ± 0.21, p = 0.64). Additionally, compared to the refraction obtained one year prior to the diagnosis of allergic conjunctivitis, patients were found to have a greater increase in cylindrical power compared to controls (0.13 ± 0.04 D vs 0.01 ± 0.02 D, p = 0.007), with no significant difference in the type of cylindrical refractive error. Conclusions Our study demonstrates that allergic conjunctivitis may prognosticate the development and progression of cylindrical refractive error in children.