The central objective of the current study was to evaluate how executive functions (EF), and specifically cognitive flexibility, were concurrently and predictively associated with anxiety and depressive symptoms in adolescence. Adolescents (N = 220) and their parents participated in this longitudinal investigation. Adolescents' EF was assessed by the Wisconsin Card Sorting Test (WCST) during the initial assessment, and symptoms of depressive and anxiety disorders were reported by mothers and youths concurrently and 2 years later. Correlational analyses suggested that youths who made more total errors (TE), including both perseverative errors (PE) and nonperseverative errors (NPE), concurrently exhibited significantly more depressive symptoms. Adolescents who made more TE and those who made more NPE tended to have more anxiety symptoms 2 years later. Structural equation modeling analyses accounting for key explanatory variables (e.g., IQ, disruptive behavior disorders, and attention deficit hyperactive disorder) showed that TE was concurrently associated with parent reports of adolescent depressive symptoms. The results suggest internalizing psychopathology is associated with global (TE) and nonspecific (NPE) EF difficulties but not robustly associated with cognitive inflexibility (PE). Future research with the WCST should consider different sources of errors that are posited to reflect divergent underlying neural mechanisms, conferring differential vulnerability for emerging mental health problems.