BACKGROUND: The negative impact of childhood overweight on psychosocial well-being has been demonstrated in a number of studies. There is also evidence that psychosocial well-being may influence future overweight. We examined the bidirectional association between childhood overweight and psychosocial well-being in children from a large European cohort. The dual aim was to investigate the chronology of associations between overweight and psychosocial health indicators and the extent to which these associations may be explained by parental education. METHODS: Participants from the IDEFICS study were recruited from eight countries between September 2007 and June 2008 when the children were aged 2 to 9.9 years old. Children and families provided data on lifestyle, psychosocial well-being, and measured anthropometry at baseline and at follow-up 2 years later. This study includes children with weight, height, and psychosocial well-being measurements at both time points (n = 7,831). Psychosocial well-being was measured by the KINDL® and Strengths and Difficulties Questionnaire respectively. The first instrument measures health-related quality of life including emotional well-being, self-esteem, parent relations and social relations while the second measures well-being based on emotional symptoms, conduct problems and peer-related problems. Logistic regression was used for modeling longitudinal associations. RESULTS: Children who were overweight at baseline had increased risk of poor health-related quality of life (odds ratio (OR) = 1.23; 95 % confidence interval (CI):1.03–1.48) measured 2 years later; this association was unidirectional. In contrast to health-related quality of life, poor well-being at baseline was associated with increased risk of overweight (OR = 1.39; 95 % CI:1.03–1.86) at 2 year follow-up; this association was also only observed in one direction. Adjustment for parental education did not change our findings. CONCLUSION: Our findings indicate that the association between overweight and psychosocial well-being may be bidirectional but varies by assessment measures. Future research should further investigate which aspects of psychosocial well-being are most likely to precede overweight and which are more likely to be consequences of overweight.