Background Many medical students may encounter a range of academic and personal challenges during their course of study, but very little is known about their experiences. Our aim was to review the literature to inform future scholarship and to inform policy change. Methods A scoping review was conducted searching PubMed, MEDLINE, EMBASE, PsycInfo, British Education Index, Web of Science and ERIC for English language primary research with no date limits. This retrieved 822 papers of which eight met the requirements for inclusion in the review. Data were independently reviewed by two researchers and underwent thematic analysis by the research team. Results Three major themes emerged. Theme 1: ‘Identity preservation’ addressed students' aim to preserve their sense of self in the face of academic difficulty and their tendency to seek support. This connected the apprehension many students expressed about their educational institutions to Theme 2: ‘The dual role of the medical school’—medical schools are required to support struggling students but are predominantly seen as a punitive structure acting as the gatekeeper to a successful career in medicine. Students' apprehension and attempts to protect their identities within this complex landscape often resulted in ‘maladaptive coping strategies’ (Theme 3). Conclusion Understanding and exploring the academic challenges faced by medical students through their own experiences highlight the need for the development of more individualised remediation strategies. Educators may need to do more to bridge the gap between students and institutions. There is a need to build trust and to work with students to enhance their sense of self and remediate approaches to engagement with learning, rather than focusing efforts on success in assessments and progression.