Background: As the gap in nutritional profiles between urban and rural rapidly reduces because of nutrition transition, rural adolescents are likely to engage in urban lifestyle behaviours.Aim: The study determined the prevalence of overweight/obesity amongst adolescents in rural high schools and the association with selected factors.Setting: Fetakgomo Municipality in rural Limpopo Province, South Africa.Methods: A cross-sectional study was conducted amongst 378 adolescents selected through multistage sampling from high schools. Data collected were socio-demography, nutritional knowledge, dietary practices and anthropometry. The International Obesity Task Force age and sex-specific body mass index (BMI) cut-off values were used to determine overweight/obesity, whilst adult BMI cut-off values were used for those ≥ 18 years. Waist-to-height ratio (WHtR) greater than 0.5 indicated abdominal obesity, as well as waist circumference (WC) and waist-to-hip ratio (WHR) above the cut-off values.Results: The proportion of overweight/obesity amongst adolescents was 35%, whilst 25% had abdominal obesity by WHR and 21% by WHtR. Multivariate logistic regression showed that being a girl (AOR = 2.9, 95% CI: 1.74–4.85), older adolescent (AOR = 3.1, 95% CI: 1.57–6.29) and living in a household with employed adults (AOR = 2.3, 95% CI: 1.19–4.51) were associated with increased odds of being overweight/obese. Eating breakfast was associated with reduced odds of being overweight/obese (AOR = 0.6, 95% CI: 0.34–0.97).Conclusion: Overweight/obesity and abdominal obesity amongst adolescents were more prevalent than underweight. The Integrated School Health Programme should have clear guidelines on food items served and sold at schools.