BackgroundMany medical residents lack ready access to social and emotional supports that enable them to successfully cope with the challenges associated with medical residency. This absence of support has been shown to lead to high levels of burnout, decreased mental wellbeing, and difficulty mastering professional competencies in this population. While there is emerging evidence that peer mentoring can be an important source of psychosocial and career-related support for many individuals, the extent of the evidence regarding the benefits of peer mentorship in medical residency education has not yet been established. We describe a protocol for a systematic review to assess the effects of peer mentoring on medical residents’ mental wellbeing, social connectedness, and professional competencies.MethodsStudies included in this review will be those that report on peer-mentoring relationships among medical residents. Quantitative, qualitative, and mixed-methods studies will be eligible for inclusion. No date or language limits will be applied. We will search EMBASE, MEDLINE, PsychINFO, Web of Science, Scopus, ERIC, Education Research Complete, and Academic Research Complete databases to identify relevant studies. Two authors will independently assess all abstracts and full-text studies for inclusion and study quality and extract study data in duplicate.DiscussionThis is the first systematic review to explicitly explore the role of peer mentoring in the context of medical residency education. We anticipate that the findings from this review will raise awareness of the benefits and challenges associated with peer-mentoring relationships, further the development and implementation of formal peer-mentoring programs for medical residents, and, through identifying gaps in the existing literature, inform future research efforts.Systematic review registrationThis protocol has not been registered in PROSPERO or any other publicly accessible registry.Electronic supplementary materialThe online version of this article (10.1186/s13643-017-0571-y) contains supplementary material, which is available to authorized users.