Overweight and obesity are serious health concerns for children. However, only a few studies have investigated the influence of gender on prevalence of overweight and obesity in children and adolescents in Nigeria. The objective of this study was to investigate gender influence on prevalence of overweight and obesity among Nigerian school children and adolescents. Information on age and gender of the participants was collected from the school register. Data on height, weight and BMI was collected using standard techniques. A total of 9,014 children and adolescents (male = 4392; female = 4622), aged 2-18 years, from 28 randomly selected schools were analyzed. Overweight and obesity were determined using the International Obesity Task Force cut-off points by age and gender. Males had higher BMI than females at age group 2-6 years, whereas females had higher BMI than males at age groups 11-14 years and 15-18 years. Females had significantly higher prevalence of overweight (P < 0.05) than males at age group 11-14 and 15-18 years. However, there was no gender difference in the prevalence of obesity from childhood through adolescence. In conclusion, BMI is larger in males in early childhood but larger in females in during adolescence. More female adolescents are at risk of obesity than males.