Introduction Micropapillary serous borderline ovarian tumours (MP-SBOTs) are an aggressive subtype of serous borderline ovarian tumours (SBOTs). Surgery is the mainstay of treatment. Radical surgery (RS, including debulking) is an alternative. However, for patients who are of reproductive age, another treatment option is fertility-sparing surgery (FSS). Up to now, the best surgical approach for MP-SBOTs and whether different procedures will have an impact on postoperative recurrence are still up for debate. This protocol outlines a systematic review and meta-analysis to investigate whether FSS adversely affected outcomes compared with RS in patients with MP-SBOTs. Additionally, we will do a prognosis analysis of BOTs with no microcapillary pattern and MP-SOBTs, if possible.Methods and analysis This protocol will consider non-randomised studies comparing outcomes in patients with MP-SBOTs treated with RS or FSS. The following databases will be searched: Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, MEDLINE, Embase Medline, PubMed, Web of Science, China Biological Medicine Database, China National Knowledge Infrastructure and Wan Fang database. We will try our best to search the grey literature to avoid missing crucial research. Data collection and extraction will be performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Risk of Bias in Non-randomised Studies of intervention will be used to assess non-randomized studies. We will assess the certainty of the evidence using the GRADEpro methodology and describe the degree of certainty of our results using suggested wording based on the GRADEpro assessment. We will conduct a meta-analysis and offer summary statistics for each result if there is enough data available. Instead, we will report the findings narratively where the data do not permit a statistical assessment.Ethics and dissemination Ethics approval was not required for this study. Results will be published through a peer-reviewed publication and communicated at scientific events once complete.PROSPERO registration number CRD42023439136.