The Cass Report aimed to provide recommendations for how services for gender diverse children and young people should be delivered in England. Our critical appraisal reveals significant methodological and conceptual flaws within the report and the research commissioned to inform the report, which included seven systematic reviews and both quantitative and qualitative primary research. Using the ROBIS tool, we identified a high risk of bias in each of the systematic reviews driven by unexplained protocol deviations, ambiguous eligibility criteria, inadequate study identification, and the failure to integrate consideration of these limitations into the conclusions derived from the evidence syntheses. We also identified potential sources of bias and unsubstantiated claims in the primary research that suggest a double standard in the quality of evidence produced for the Cass Report compared to quality appraisal in the systematic reviews. We discuss these issues in relation to how evidence regarding gender affirming care is framed, the wider political context, and the future for gender affirming care. To uphold evidence-based medicine, future gender-affirming care research must generate robust observational data, involve transgender communities, and prioritise patient-centred outcomes, ensuring validity, generalisability, and cultural relevance. The Cass Report’s recommendations, given its methodological flaws and misrepresentation of evidence, warrant critical scrutiny to ensure ethical and effective support for gender-diverse youth.