Background: Internationally, the demand for gender-affirming care has increased exponentially in recent years. The clinical presentation of those seeking care has changed with an increase in transmasculine and non-binary identities and a decrease in the average age of those seeking care. Healthcare navigation remains complicated for this population and warrants further investigation in light of ongoing changes in the field. This paper presents a protocol for a scoping review to map and synthesise the academic and grey literature on instruments used to assess healthcare navigation and access for transgender and non-binary individuals seeking gender-affirming care.Methods: This review will search databases (PsychINFO, CINAHL, Medline, and Embase.) and grey literature sources. In line with the methodological framework for scoping reviews, the following six stages will be undertaken: (1) identifying the research question, (2) identifying relevant studies, (3) study selection, (4) charting the data, (5) collating, summarising and reporting results and (6) consultation. The PRISMA Extension for Scoping Reviews (PRISMA-ScR): checklist and explanation will be utilised and reported. The research team will undertake the study as outlined in this protocol and an expert panel of young transgender and non-binary youth will oversee the project through patient and public involvement.Conclusions: This scoping review has the potential to inform policy, practice, and future research through enhanced understanding of the complex interplay of factors that impact healthcare navigation for transgender and non-binary people seeking gender-affirming care. The results from this study will inform further research into healthcare navigation considerations generally and will inform a research project entitled “Navigating access to gender care in Ireland—a mixed-method study on the experiences of transgender and non-binary youth”.