Background: The stressful nature of medical training and other work-related factors put postgraduate medical trainees at high risk of burnout and poor psychological wellbeing. This has negative implications for patient care and the effectiveness of the healthcare system. The structure of the healthcare system and postgraduate medical education in Australia is different to that of other countries. Whilst a significant body of research exists on burnout and wellbeing in trainees in the USA, evidence specific to Australian trainees is lacking. The aim of this review is to synthesise the current knowledge on the factors that impact burnout and psychological wellbeing in Australian postgraduate medical trainees. Methods/design: A systematic review will be conducted across eight digital databases: Academic Search Complete, MEDLINE, Embase, Web of Science, PsychInfo, Scopus, CINAHL Plus and Informit Health Collection. Peer reviewed empirical studies and relevant grey literature published after 2000 that address an aspect of burnout or psychological wellbeing in Australian postgraduate medical trainees will be included. Two reviewers will independently review each article against the inclusion and exclusion criteria, with disagreements resolved via discussion and consensus. Data will be extracted using a standard form and quality will be assessed using the assessment tools available from the Joanna Briggs Institute. A thematic narrative synthesis of the studies will be presented, along with an assessment of current gaps in the literature and areas for future research. Discussion: This review will be the first to integrate the evidence on burnout and psychological wellbeing specific to Australian postgraduate medical trainees. The findings will contribute to a better understanding of the factors that impact burnout and psychological wellbeing in this population and will lay the foundation for future research into appropriate strategic interventions. Systematic review registration: This protocol has been registered in the International Prospective Register of Systematic Reviews (PROSPERO: CRD42020203195).