This pilot study examined associations between transdiagnostic symptoms and parent-perceived parent-child relationship quality in treatment-seeking families of children with neurodevelopmental disabilities, and interactions among clinical symptoms and cognitive functioning. Sixty-three children between 8 to 13 years of age and their caregivers were assessed at baseline while seeking cognitive behaviour therapy for emotion regulation and mental health difficulties. Diagnoses included autism, ADHD, cerebral palsy, and learning disability, with 52% of children having multiple diagnoses. Parent-perceived parent-child relationship quality was assessed by the Positive Affect Index, autism symptoms (e.g., social communication, repetitive behaviours) by the Social Responsiveness Scale, Second Edition, mental health (i.e., internalizing problems, externalizing problems, behavioural symptoms) by the Behaviour Assessment Scale for Children, Third Edition, and IQ by the Weschler Abbreviated Scale of Intelligence, Second Edition. Results revealed that higher IQ scores and greater social communication challenges, externalizing problems, and behavioural symptoms, were associated with lower parent-child relationship quality. Interaction effects were found between IQ and social communication challenges, reflecting significantly stronger relationships between social communication challenges and lower parent-child relationship quality in the context of higher IQ. Understanding the interactions between cognitive functioning and social communication challenges can help to inform individualized supports, and advocate for a transdiagnostic approach to intervention.