BACKGROUND: This study assessed gender-specific associations between body mass index (BMI) and social-emotional wellbeing (SEW) among differentially active seven-year-old children. METHODS: Data are from wave four of the UK Millennium Cohort Study, collected in 2007-08. Children wore an ActiGraph accelerometer for seven consecutive days and measures of stature and body mass were taken. BMI was calculated from stature and body mass (kg/m2). Parents/carers completed the strengths and difficulties questionnaire (SDQ). A total of 6011 children (3073 girls) had completed data. Mean minutes per day spent in moderate-to-vigorous intensity physical activity (MVPA) were calculated for each child. Gender-specific MVPA quartile cut-off values categorized boys and girls separately into four graded groups representing the least (Q1) through to the most active (Q4) children. Adjusted linear regression analyses examined associations between BMI and SDQ scores. Gender-specific analyses were conducted separately for MVPA quartiles. RESULTS: BMI was positively associated with peer problems for Q1 and Q2 boys and girls, conduct problems for Q2 and Q4 boys, emotional problems and prosocial behaviour for Q2 boys and total difficulty scores for Q1 girls and Q2 boys (P < 0.05). CONCLUSIONS: Our results revealed that BMI was positively associated with SEW difficulties among the low active children but not the high active children. Further research examining the concurrent effect of diet and MVPA on child weight status and SEW is needed.