There is a lack of research on associations of social jetlag with eating behaviours and obesity among adolescents. We examined the associations of social jetlag with eating behaviours and BMI in adolescents before and after adjustment for potential confounders. Self-report data were collected from 3060 adolescents (48·1 % female, mean age 15·59 (sd 0·77) years) from the Fragile Families and Child Wellbeing Study. In regression models, social jetlag predicted odds of consumption of breakfast, fruits/vegetables, fast food and sweetened drinks and BMI percentile. Primary models adjusted for school night sleep duration, sex, age, household income and youth living arrangements; secondary models further adjusted for race/ethnicity. In fully adjusted models, greater social jetlag was associated with lower odds of consumption of breakfast (OR = 0·92, P = 0·003) and fruits/vegetables (OR = 0·92, P = 0·009) and higher odds of consumption of fast food (OR = 1·18, P < 0·001) and sweetened drinks (OR = 1·18, P < 0·001). Social jetlag was positively associated with BMI percentile after additional adjustment for eating behaviours (b = 0·84, P = 0·037), but this relationship was attenuated after adjustment for race/ethnicity (b = 0·72, P = 0·072). Ethnoracial differences in social jetlag may attenuate the association of social jetlag with BMI and should be considered in future studies of circadian misalignment, eating behaviours and obesity markers.