Family functioning and age of onset of weight problems have been identified as correlates of psychopathology in the adult obesity literature, but have not sufficiently been investigated in overweight adolescents’ functioning. This study aimed to explore the effects of individual perceptions of family functioning (FF) in adolescents and parents, as well as the influence of discrepancies between family members in perceptions of FF, on adolescent internalizing symptoms. A secondary aim included examining whether earlier age of onset of weight problems predicted adolescents’ experience of internalizing symptoms. Participants included two samples of families who sought family-based pediatric weight management treatment: 1) 626 mother-adolescent dyads; and 2) 396 mother-adolescent-father triads (“intact families”). Adolescent reports of depression, anxiety, and worthlessness were examined along with adolescent and parent reports of family cohesion and adaptability. Structural equation modeling was used to examine predictive relationships between FF (both perceptions and discrepancies), age of onset, and internalizing symptoms for each sample and adolescent gender. The best-fitting models were essentially identical for both samples across gender. Findings illustrate that: 1) parental perceptions of decreased FF predicted psychological distress in both overweight males and female adolescents; 2) adolescents suffering from internalizing symptoms were more likely to report negative perceptions of FF; and 3) greater parental-adolescent discrepancies were predicted by adolescents’ internalizing symptoms. Earlier age of onset, however, was not found to predict increased internalizing symptoms. Finally, parental perceptions of FF were found to predict adolescent perceptions of FF for adolescents in intact families only. These findings provide evidence that adolescent weight management programs and other health care providers should address the significant influence that poor family functioning plays in predicting overweight adolescents’ internalizing symptoms.