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Background There are stark ethnic inequalities in the prevalence of UK childhood obesity. However, data on adolescent overweight in different ethnic groups are limited. This study assessed ethnic inequalities in overweight prevalence during mid-adolescence using body mass index (BMI) and explored the contribution of socioeconomic and behavioural factors. Methods We analyzed data from 10 500 adolescents aged between 13 and 15 years who participated in sweep six of the Millennium Cohort Study. Ethnic inequalities in overweight and mean BMI were assessed using multiple regression models. Results were stratified by sex and adjusted for socioeconomic and behavioural factors. Results Black Caribbean males had significantly higher BMI than White males after full adjustment [excess BMI 2.94, 95% confidence interval (CI) 0.70–5.19] and were over three times more likely to be overweight [odds ratio (OR): 3.32, 95% CI 1.95–5.66]. Black Africans females had significantly higher BMI compared with White females (excess BMI 1.86, 95% CI 0.89–2.83; OR for overweight 2.74, 95% CI 1.64–4.56), while Indian females had significantly lower BMI compared with White females (reduced BMI −0.73, 95% CI −1.37 to −0.09). Socioeconomic and behavioural factors often considered to be associated with overweight were more prevalent in some ethnic minority groups (lower socioeconomic position, lack of breakfast consumption, low fruit and vegetable intake, high sugar-sweetened beverage and fast-food consumption, and infrequent physical activity), but adjustment for these factors did not fully explain ethnic differences in overweight/BMI. Conclusion Ethnic inequalities in overweight prevalence are evident in mid-adolescence and vary according to sex. Differences in overweight/BMI between ethnic groups were not fully accounted for by socioeconomic or behavioural factors.