IntroductionGender Identity Development Services (GIDS) worldwide have experienced a significant increase in referrals in recent years. However, little is currently known about the experiences of the children and young people (CYP) and their families attending these services and the influences on their well-being. Most published qualitative studies have explored gender identity and gender questioning CYP from either a parental perspective or in an adolescent sample. Consequently, there is a need for research to explore the voices of younger children and adolescents who are referred to GIDS. This study aims to address current gaps in understanding of the experiences of CYP referred to the UK GIDS, specifically regarding the personal, familial, educational, and social contexts in which CYP and their parents/caregivers are navigating gender identity, social and physical transition, and the healthcare system.Methods and analysisA prospective longitudinal qualitative study examining the experiences and well-being of CYP referred to the UK GIDS. A purposive sample of up to 40 families will be recruited. Families will be eligible for the study if the child or young person was aged 3–14 years at the time of referral to the GIDS. Semistructured interviews will be conducted with both the child/young person and their parents/caregivers. Analysis of anonymised interview transcripts will be interpretive and pluralistic, informed by both narrative and thematic approaches. This study forms part of a wider programme of research investigating longitudinal outcomes of gender identity in children (the LOGIC Study).Ethics and disseminationThe proposed study has been approved by the UK Health Research Authority and London–Hampstead Research Ethics Committee as application 19/LO/0857. The study findings will be published in peer-reviewed journals and presented at both conferences and stakeholder events.