ObjectivesUndernutrition is a major public health concern, particularly in children. The burden is higher in developing countries. Undernutrition is considered when there is one or more of the following: stunting, underweight, or wasting. Childhood undernutrition can have numerous long-term effects: a lower physical capacity for work, lower intellectual quotients, greater risk for morbidity and mortality, and cognitive impairment. Undernourished children also can have poor cognitive scores, a high absenteeism rate, and high class repetition compared with non-undernourished children. The aim of this study was to assess undernutrition and its associated factors among public and private primary school children in Gondar town, northwest Ethiopia. MethodsA school-based, cross-sectional study was conducted from March 5 to April 9, 2019. A multistage sampling technique was applied to select study participants. A simple random (lottery) sampling method was used to select seven public schools and five private schools. Systematic random sampling was used to select 774 study participants. The data were collected through face-to-face interviews. Multivariable logistic regressions were conducted to identify factors associated with undernutrition. The World Health Organization (WHO) AnthroPlus software was used to determine the status of undernutrition. Participants with a Z-score less than –2 were considered to be undernourished. Statistical significance was declared at P < 0.05 and odds ratios (ORs) were reported with a 95% confidence interval (CI). ResultsThe prevalence of undernutrition was higher among public school children (37.1%) than those attending private schools (28.3%). Not having family car (adjusted OR [aOR], 0.28; 95% CI, 0.09–0.84), snack frequency no more than twice a day (aOR, 5.29; 95% CI, 1.37–20.37), and vigorous intensity sports (aOR, 0.53; 95% CI, 0.32–0.91) were significantly associated with undernutrition among public primary school students. Family income below the median (aOR, 2.12; 95% CI, 1.23–3.53), no preference for sweets (aOR, 0.59; 95% CI, 0.36–0.97), and not habits while reading (aOR, 0.42; 95% CI, 0.19–0.89) were the factors significantly associated with undernutrition among private primary school students. ConclusionThe prevalence of undernutrition was high. Children in public schools were highly vulnerable to undernutrition compared with those in private schools. Not having a family car, snack frequency no more than twice daily, and vigorous intensity sports increase the risk for undernutrition among public school children. Family income below the median, not preferring sweets, and not having a habit of eating while reading increase the risk for undernutrition among private school children. It is better to give attention to healthy dietary habits and healthy lifestyles to reduce childhood undernutrition.