Abstract Background Gender-affirming hormone (GAH) therapy aims to support the transition of transgender people to their gender identity. GAHs can induce changes in their secondary sex characteristics such as the development of breasts in transgender females and increased muscle mass in transgender males. The face and its surrounding tissues also have an important role in gender confirmation. The aim of this scoping review is to systematically map the available evidence in order to provide an overview of the effects of GAH therapy on the hard and soft tissues of the craniofacial complex in transgender people. Methods/design The Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA) extension for Scoping Reviews was consulted for reporting this protocol. The methods were based on the Arksey and O’Malley’s framework and the Reviewer’s Manual of the Joanna Briggs Institute for conducting scoping reviews. Ten transgender people were involved in the development of the primary research question through short interviews. The eligibility criteria were defined for transgender people undergoing GAH therapy and for quantitative and qualitative outcomes on the hard and soft tissues of the craniofacial complex. Eligible sources of evidence include observational, experimental, qualitative, and mixed method studies. No exclusion criteria will be applied for the language of publication and the setting. To identify eligible sources of evidence, we will conduct searches from inception onwards in PubMed, Embase.com, the Cochrane Library, Web of Science Core Collection, Scopus, CINAHL, LIVIVO, and various grey literature sources such as Google Scholar. Two reviewers will independently select eligible studies in these information sources and will subsequently conduct data extraction. The same operators will chart, categorize, and summarize the extracted data. A narrative summary of findings will be conducted. Frequency counts of quantitative and qualitative data on items such as concepts, populations, interventions, and other characteristics of the eligible sources will be given. Where possible, these items will be mapped descriptively. Discussion We chose the scoping review over the systematic review approach, because the research questions are broad-spectrum and the literature is expected to be widely scattered. No systematic review has previously assessed this topic. Identifying knowledge gaps in this area and summarizing and disseminating research findings are important for a wide spectrum of stakeholders, in particular, for transgender people who want to undergo additional interventions such as plastic or orthognathic surgery or orthodontics. Systematic review registration This protocol was registered in the Open Science Framework: https://osf.io/e3qj6