Introduction. Childhood overnutrition is a public health problem in low- and middle-income countries because its effect is likely to progress into adulthood that results in developing noncommunicable diseases at a younger age. There is no such previous comparative study that investigated this issue. Therefore, the aim of this study is to assess the prevalence and associated factors of overnutrition among government and private primary school students in Gondar town, northwest Ethiopia. Methods. Institution-based comparative cross-sectional study was conducted from March 5 to April 9, 2019. A multistage sampling technique was used to select 736 participants. Data were collected through face-to-face interview. Data was entered into EPI-info version 7.2.1.0 and exported to SPSS version 20 for analysis. Bivariable and multivariable logistic regressions were carried out to identify associated factors with overnutrition. Statistical significance was declared using p value< 0.05. Results. The overall prevalence of overnutrition was 9.1%. The prevalence was higher among private schools (51 (14%)) than government (16 (4.3%)). Eating habit while watching television (AOR = 4.08, 95%CI: 1.10–15.16) and not having close friend (AOR = 3.72, 95%: CI: 1.21–2 11.48) were significantly associated with overnutrition in the government schools, while no father education (AOR = 2.59, 95%:CI:1.05–6.39), sweet food preference (AOR = 2.86, 95%:1.19–6.87), fat consumption more than three days per week (AOR = 3.79, 95%CI:1.61–8.91), eating habit while reading (AOR = 4.95, 95%CI:2.29–10.70), and vigorous-intensity sports (AOR = 2.23, 95%:1.02–4.86) were associated with overnutrition in private schools. Conclusion. Prevalence of overnutrition was higher among private than government schools. Hence, it requires attention through creating awareness about healthy diet, healthy lifestyle, and physical activity in collaboration with health and education sectors.