IntroductionGender identity development services (GIDS) worldwide have seen a significant increase in referrals in recent years. Many of these referrals consist of children and young people (CYP) who experience gender-related distress. This study aims to improve understanding of outcomes of CYP referred to the UK GIDS, specifically regarding gender identity, mental health, physical health and quality of life. The impact of factors such as co-occurring autism and early social transition on outcomes over time will be explored.Methods and analysisThis is a prospective cohort study of CYP aged 3–14 years when referred to the UK GIDS. Eligible participants will be ≤14 years at the time their referral was accepted and will be on the waitlist for the service when baseline measures are completed. Children aged under 12 years will complete the measures in an interview format with a researcher, while young people aged 12 years and over and their parents/caregivers will complete online or paper-based questionnaires. Participants will complete follow-up measures 12 months and 24 months later. The final sample size is expected to be approximately 500. Logistic regression models will be used to explore associations between prespecified explanatory variables and gender dysphoria. Appropriate regression models will also be used to investigate explanatory variables for other outcomes. Subgroup analyses based on birth-assigned gender, age at referral and co-occurring autistic traits will be explored.Ethics and disseminationThe study has been approved by the Health Research Authority and London – Hampstead Research Ethics Committee (reference: 19/LO/0857). The study findings will be published in peer-reviewed journals and presented at both conferences and stakeholder events. Findings will be used to inform clinical practice.