Introduction Very little is known about the prevalence of refractive errors among children in Kazakhstan. The aim of this study was to investigate the prevalence of refractive errors and risk factors of myopia among schoolchildren in Almaty, Kazakhstan. Methods In the cross-sectional study of 2293 secondary school students (age 6–16), we examined cycloplegic autorefraction and offered a questionnaire in three age groups: 1st grade (N = 769), 5th grade (N = 768) and 9th grade (N = 756). The questionnaire covered main risk factors such as parental myopia, screen time, time outdoors, sports activities, near work, gender, grade, and school shift. Adjusted logistic regression analysis was applied to test the association of risk factors with myopia. Results The mean spherical equivalent (SER) was -0.54 ± 1.51 diopters (D). The overall prevalence of refractive errors was 31.6% (95% confidence interval (CI) 29.7; 33.5); myopia 28.3% (95% CI 26.5; 30.1); hyperopia 3.4% (95% CI 2.7–4.1) and astigmatism 2.8% (95% CI 2.1; 3.5). In the multivariate adjusted regression analysis, higher class level (5th grade (odds ratio (OR) 1.78; 95% CI 1.26; 2.52) and 9th grade (OR 3.34; 95% CI 2.31; 4.82)) were associated with myopia, whereas outdoors activity more than 2 hours a day (OR 0.64; 95% CI 0.46; 0.89) and sports (OR 0.70; 95% CI 0.52; 0.93) were associated with a lower incidence of myopia. Conclusions Myopia is a leading refractive error in schoolchildren in Almaty, Kazakhstan. Myopia prevention measures, including more time outdoors, should guide public health interventions in this population.