Background: Double burden of malnutrition (DBM) is the co-existence of overweight/obesity and undernutrition. Rising prevalence rates of childhood overweight/obesity in Nigeria have been reported, whilst undernutrition continues to be prevalent. This study aimed to estimate the prevalence and distribution of underweight, stunting, thinness, overweight/obesity, and DBM among school-aged children and adolescents in two Nigerian States. Methods: This was a community-based cross-sectional study carried out in Osun and Gombe States. A total of 1,200 children aged 6 – 19 years were recruited using multi-stage sampling technique. Weight, height and data on demographic, socio-economic, household/family characteristics of the children were collected using structured interviewer administered questionnaires. Nutritional status was calculated using the WHO 2007 reference values using BMI-for-age (thinness, overweight/obesity), height-for-age (stunting) and weight-for-age (underweight). DBM was described at the population and individual levels. Results: The mean age of the respondents was 11.6 ± 3.8 years. The overall prevalence rate of stunting was 34.9%, underweight was 13.5%, thinness was 10.3% and overweight/obese was 11.4% and 4.0% had individual level DBM, which typifies the DBM at individual and population levels. These rates differed significantly across demographic, socio-economic and household/family characteristics (p < 0.05). Gombe State, which is in the Northern part of Nigeria, had significantly higher burden of stunted, underweight and thin children than Osun State, while Osun State, in the Southern part of Nigeria, had a significantly higher burden of overweight/obesity. Conclusions: The study found evidence of DBM both at population and individual levels. The overall prevalence rates of stunting, underweight, thinness and overweight/obesity in this study were high, and they differed significantly across the demographic, socio-economic and household/family characteristics. There is the need for government and all other stakeholders to design nutritional educational programmes that will target both under- and over-nutrition among older children in the different contexts.