Childhood obesity and mental disorders often co-exist. To date, most of the studies are cross-sectional, involve the assessment of a specific disorder, and rely on self-report questionnaires. This study aimed to provide a comprehensive psychological assessment to examine the concurrent and prospective association between childhood obesity and mental health problems. We compared 34 children with obesity with 37 children with normal weight at baseline, and at a five-year follow-up, to examine the development of mental health disorders from childhood (8-12 years) to adolescence (13-18 years). Both assessments included a clinical interview and self-reported measures of psychosocial and family markers. Findings showed that the obesity group had a higher prevalence of mental disorders, and psychological comorbidity increased in five years. Prospectively, childhood obesity was associated with a psychological diagnosis in adolescence. Moreover, the obesity group displayed higher severity of symptoms at both times. Finally, body esteem contributed to predicting mental health disorders in adolescence regardless of weight status, while eating symptomatology was a specific marker for the obesity group. Therefore, in the management of childhood obesity is suggested to address also psychosocial variables such as weight-related teasing and body esteem, to prevent the onset or development of mental health problems.