Background: Globally, miniscule improvements have been implemented regarding equality, inclusion, access, and protection of people with diverse gender identities whilst accessing health care facilities of which transgender youth form part. Literature has highlighted that the care transgender youth receive at health care facilities can result in positive or negative outcomes. School-going transgender youth constitute a unique group whose experiences at health care facilities warrant ongoing research. Hence, the objective of this scoping review is to systematically map evidence of school-going transgender youths' experiences at health care facilities regarding service delivery, support, and policies and to identify literature gaps that could inform future research. Methods: We will conduct a scoping review, using peer-reviewed journal articles that present literature on schoolgoing transgender youths' experiences at health care facilities. Searches for relevant articles will be conducted on the following databases: PubMed, Cochrane Library, Campbell collaboration, Scopus, Embase, and MEDLINE. Additional searches will be conducted on institutional websites or web-based search portals. Two reviewers will independently extract data from all relevant search engines incorporating the study objective, research questions, and eligibility criteria. The inclusion criteria include published full-text qualitative, quantitative, and mixed-method studies that address the topic with no language and publication year limitations to reflect a comprehensive range of literature that includes the implementation of the SDGs. All literature that does not meet the inclusion criteria will be excluded. The quality of included studies will be appraised using the mixed methods appraisal tool (MMAT)version 2018. Discussion: We anticipate mapping the experiences of school-going transgender youth at health care facilities. Once summarized, the data could be useful to clinical educators, health workers, policy makers, and guide future research to ensure that the human and patients' rights of transgender youth, are globally acknowledged, protected, and respected within health care facilities.