Very little is known about the differences of the neurocognitive functioning of Attention Deficit Hyperactivity Disorder (ADHD) and Paediatric Bipolar Disorder (PBD), since current studies do not agree on a differentiation of Executive Function (EF) between the two disorders. The aim of this study was to determine the EF deficits associated with symptomatology of ADHD and the PBD phenotype. Participants were 76 children/adolescents aged 6-17 years and their parents, submitted to a diagnostic interview and a tool for assessing EF, Behaviour Rating Inventory of Executive Function. Structural Equation Modeling was used to examine associations between symptoms of ADHD and the PBD phenotype, and the EF. A model for parents and a model for children/adolescents were performed. The model indexes showed a satisfactory fit. ADHD was found to be associated with deficits in all areas of EF, especially when the predominant symptom is inattention. The presence of symptoms of PBD phenotype was associated only with difficulties in finding new strategies to solve problems and inhibiting new behaviour. The article concluded that the presence of ADHD symptoms is associated with cognitive deficits different from those that may occur with PBD symptoms. It is advisable that professionals consider patients' neurocognitive profiles in order to achieve an appropriate differential diagnosis.