Abstract Background Data from studies with undergraduate and postgraduate taught students suggest that they are at an increased risk of having mental health problems, compared to the general population. By contrast, the literature on doctoral researchers (DRs) is far more disparate and unclear. There is a need to bring together current findings and identify what questions still need to be answered. Methods We conducted a mixed methods systematic review to summarise the research on doctoral researchers’ (DRs) mental health. Our search revealed 52 articles that were included in this review. Results The results of our meta-analysis found that DRs reported significantly higher stress levels compared with population norm data. Using meta-analyses and meta-synthesis techniques, we found the risk factors with the strongest evidence base were isolation and identifying as female. Social support, viewing the PhD as a process, a positive student-supervisor relationship and engaging in self-care were the most well-established protective factors. Conclusions We have identified a critical need for researchers to better coordinate data collection to aid future reviews and allow for clinically meaningful conclusions to be drawn. Systematic review registration PROSPERO registration CRD42018092867