Research suggests an overrepresentation of autism spectrum diagnoses (ASD) or autistic traits in gender diverse samples, particularly in children and adolescents. Using data from the GENTLE (GENder identiTy Longitudinal Experience) Cohort at the Gender Diversity Service at the Perth Children's Hospital, the primary objective of the current retrospective chart review was to explore psychopathology and quality of life in gender diverse children with co-occurring ASD relative to gender diverse children and adolescents without ASD. The Social Responsiveness Scale (Second Edition) generates a Diagnostic and Statistical Manual of Mental Disorders (DSM-5) score indicating a likely clinical ASD diagnosis, which was used to partition participants into two groups (indicated ASD, n = 19) (no ASD indicated, n = 60). Indicated ASD was far higher than would be expected compared to general population estimates. Indicated ASD on the Social Responsiveness Scale 2 (SRS 2) was also a significant predictor of Internalising behaviours (Anxious/Depressed, Withdrawn/Depressed, Somatic Complaints, Thought Problems subscales) on the Youth Self Report. Indicated ASD was also a significant predictor of scores on all subscales of the Paediatric Quality of Life Inventory. The current findings indicate that gender diverse children and adolescents with indicated ASD comprise an especially vulnerable group that are at marked risk of mental health difficulties, particularly internalising disorders, and poor quality of life outcomes. Services working with gender diverse young people should screen for ASD, and also provide pathways to appropriate care for the commonly associated mental health difficulties.