Over the past three decades, our understanding of the nature, assessment and treatment of childhood mental disorders has increased significantly. Some of the most recent advances come from transdiagnostic and neuropsychological-based approaches. While the relationship of similar neuropsychological deficits with some mental disorders, such as neurodevelopmental and severe mental disorders like schizophrenia or bipolar disorder, is widely established, there is more controversy about their relationship with the so-called internalizing and externalizing disorders. In this article, our goal was to highlight the potential of incorporating cognitive strategies from integrative neuropsychological and transdiagnostic approaches to improve the effectiveness of empirically-supported cognitive-behavioral therapy for internalizing and externalizing mental disorders in childhood and adolescence. The results of the present work indicate that the vast majority of internalizing disorders, including the presence of anxiety, depressive, trauma-and stress-related, and obsessive-compulsive and related disorders, as well as externalizing symptoms (corresponding to conduct disorder and ODD), present neuropsychological deficits and that their consideration may be relevant to improve the effectiveness of psychotherapeutic interventions in children and adolescents by incorporating neuropsychology-based assessment and treatment tools. The inclusion of neuropsychological support strategies in therapy for childhood mental disorders implies an advance and has clear implications for the enhancement of psychological care for childhood mental disorders.