Background: Due to vulnerabilities resulting from disparities in socio-economic status (SES), most nutrition and health interventions are targeted at children in public schools. This study was conducted to investigate the determinants of malnutrition among pupils attending public and private schools in the Hohoe municipality, Ghana. Methods: School-based cross-sectional survey, which used a multi-stage random sampling technique to select 633 pupils, aged 3-12 years enrolled in 14 public and seven private schools. Data was collected through face-to-face interviews using semi-structured questionnaire. Type of school attended was used as proxy of SES of the pupils. Weight, height and mid upper-arm circumference were measured and used to generate underweight, stunting, thinness and obesity levels using WHO Antroplus and STATA 12.1. Mutually adjusted simple and multinomial logistic regressions were performed to determine associations between explanatory and dependent variables. Results: Underweight (13 % vs. 2 %, p = <0.0001), stunting (12 % vs. 3 %, p = <0.0001) and thinness (8 % vs. 1.4 %, p < 0.0001) were higher among pupils attending public schools compared to their private schools counterparts. Public school pupils had increased likelihood for underweight (AOR = 7.5; 95 % CI = 2.4-23; p = 0.001) and an increase risk for thinness (RR = 4.7; 95 % CI = 1.5-21.2; p = 0.028) but had decrease risk for overweight (RR = 0.3; 95 % CI = 0.1-1; p = 0.043). Overweight (9 %) was higher among private schools pupils compared to public schools (3 %). Underweight (14 % vs. 6 %), stunting (14 % vs. 4 %) and thinness (8 % vs. 4 %) were higher among pupils in rural schools compared to urban dwellers. Rural schools children were twice likely to become stunted (AOR = 2.6; 95 % CI = 1.0-6.4; p = 0.043). However among pupils attending schools in urban areas, the prevalence of overweight was 7 % compare to 1 % in rural areas. Pupils who consumed only two meals per day were more likely to be underweight (AOR = 6.8; 95 % CI = 1.4-32.2; p = 0.016), stunted (AOR = 7.2; 95 % CI = 1.2-43.7; p = 0.033) and thin (RR = 9.4; 95 % CI = 2.0-47.8; p = 0.007) compared to those who had at least three square meals daily. Conclusion: Both under nutrition and over-nutrition were common among the school pupils but overweight appeared largely driven by high SES and urbanization while under nutrition was associated with low SES and rural residency. Interventions targeting school children should aim at reducing poverty and hunger as these factors remain as underlying causes of malnutrition in childhood.