Objective: To appraise the methodological quality of studies on the prevalence of psychiatric comorbidities for children presenting with gender dysphoria, including diagnosis and management. Study design: A systematic review of 15 articles on psychiatric comorbidities for children diagnosed with gender dysphoria between the ages of two–12 years. Data sources: A systematic literature search of Medline, PsychINFO, CINAHL, Scopus and Web of Science for English-only studies published from 1980 to 2019, supplemented by other sources. Of 736 studies, 721 were removed following title, abstract or full-text review. Results: Ten studies were retrospectively-oriented clinical case series or observational studies. There were few randomised, controlled trials. Over 80% of the data came from gender clinics in the United States and the Netherlands. Funding or conflicts of interest were often not declared. Mood and anxiety disorders were the most common psychiatric conditions studied. There was little research on complex comorbidities. One quarter of studies made a diagnosis by a comprehensive psychological assessment. A wide range of psychological tests was used for screening or diagnostic purposes. Over half of the studies diagnosed gender dysphoria using evidence-based criteria. A quarter of the studies mentioned treating serious psychopathology prior to addressing gender dysphoria. KEY POINTS What is already known about this topic: Children with gender dysphoria are likely to experience profound psychological and physical difficulties. Gender clinics around the world have different ways of assessing and treating children with gender dysphoria. Children often rely on caregivers and health professionals to make treatment decisions on their behalf. What this topic adds: Children with gender dysphoria often experience a range of psychiatric comorbidities, with a high prevalence of mood and anxiety disorders, trauma, eating disorders and autism spectrum conditions, suicidality and self-harm. It is vitally important to consider psychiatric comorbidities when prioritising and sequencing treatments for children with gender dysphoria. The development of international treatment guidelines would provide greater consistency across diagnosis, treatment and ongoing management.