The aim of this study was to assess overweight and obesity and associated factors in school-going adolescents in low income African countries (Ghana, Uganda). The total sample included 5,613 school children aged 13 to 15 years from nationally representative samples from two African countries. Bivariate and multivariable analyses were conducted to assess the relationship between dietary behavior, substance use, physical activity, psychosocial factors and overweight or obesity. The prevalence of overweight and obesity was determined based on self-reported height and weight and the international child body mass index standards. Results indicate a prevalence of overweight or obesity of 10.4% among girls and 3.2% among boys, and 0.9% and 0.5% obesity only among girls and boys, respectively. Among girls smoking cigarettes and loneliness and among boys smoking cigarettes were found to be associated with overweight or obesity in multivariable analysis. Overweight status was not associated with the intake of fruits, vegetables, and sedentary behavior. Low prevalence rates of overweight or obesity were found in Ghana and Uganda. Smoking cessation and social programs could be integrated into strategies to prevent and treat overweight and obesity in youth.