There are widespread differences in overweight/obesity prevalence in children, and understanding the reasons for this is very important. The present study aims: (I) to conduct a meta-analysis on overweight/obesity prevalence in Portuguese children; (II) to identify differences in biological and behavioural characteristics between normal-weight and overweight/obese children; and (III) to investigate the importance of individual- and school-level correlates of variation in children's BMI using multilevel modelling. A search was done for all published papers including Portuguese children during the last decade; further, 686 Portuguese children (9-11 years old) were sampled and their BMI, family income, maturity offset, nutritional habits, physical activity, sedentariness, sleep time, and school environment information were collected. Results showed a stabilization of overweight/obesity during the last decade, 30.6% (95%CI: 0.287-0.34) for boys, 28.4% (95%CI: 0.23-0.35) for girls, and 30.3% (95%CI: 0.27-0.34) for boys and girls together. Differences between weight groups were only found in individual-level biological traits. The multilevel analysis did not identify significant contributions of school-level variables to children's BMI variation. In conclusion, no increase was found in the prevalence of overweight/obesity among Portuguese children since 2000. Normal-weight and overweight/obese children only differ in individual-level characteristics, and school context variables were not related to variation in BMI.