The Strengths and Difficulties Questionnaire (SDQ) is a worldwide questionnaire used for the early identification of behavioural/emotional symptoms in children and adolescents with neuropsychiatric disorders. Although its prognostic power has been studied, it has not yet been tested whether SDQ: (i) can identify pathognomonic symptoms across a variety of neurodevelopmental and neuropsychiatric disorders, (ii) can capture emotional and behavioural problems associated with the main diagnosis, as well as shared transdiagnostic dimensions, and (iii) can detect changes in symptomatology with age. The present study evaluated nearly 1000 children and adolescents overall with Global Developmental Delay (GDD), Intellectual Disability (ID), Language Disorder (LD), Specific Learning Disorder (SLD), Autism Spectrum Disorder (ASD), Attention Deficit/Hyperactivity Disorder (ADHD), Mood Disorder (MD), Anxiety Disorder (AD), and Eating Disorders (ED). We found that SDQ: (i) can identify the core symptoms in children with ASD, ADHD, MD, and AD via specific subscales; (ii) can capture the associated emotional and behavioural symptoms in children with LD, GDD, ID, SLD, and ED; and (iii) can detect changes in the symptomatology, especially for GDD, LD, ASD, ADHD, and AD. SDQ is also able to recognise the transdiagnostic dimensions across disorders. Our results underscore the potential of SDQ to specifically differentiate and identify behavioural/emotional profiles associated with clinical diagnosis.