Objective To assess the strabismus prevalence and associated factors among children aged ≤15 years. Methods This hospital-based cross-sectional study was conducted from March 2017 to October 2017 in the Department of Ophthalmology & Optometry, Hawassa University Comprehensive Specialized Hospital. Interviewer-administered questionnaires were used to collect relevant data and clinical examinations were performed for patient diagnosis. Results Overall, 582 children participated in the study (response rate, 97%). The prevalence of childhood strabismus was 17.9% [95% confidence interval: 14.6–21.1]. Additionally, 9.6%, 16.7%, and 9.6% of the children had anisometropia, amblyopia, and dense cataract, respectively. Among the 16.7% of children with amblyopia, 56.7% had strabismus; among the 22.5% of children with clinically significant refractive error, 52.7% had strabismus. Moreover, among the 9.6% of children with anisometropia, 58.9% had strabismus. The presence of amblyopia (adjusted odds ratio [95% confidence interval]: 3.9, 1.7–8.6), age <5 years (13.5 [5.0–36.1]), age 5 to 10 years (6.1 [2.3–16.3]), and clinically significant refractive error (13.3 [5.8–30.6]) were significantly associated with childhood strabismus. Conclusions The prevalence of strabismus was relatively high among patients in this study. Early screening for childhood strabismus is essential. A well-controlled community-based study is needed to confirm strabismus prevalence and predictors.