Acute basilar artery occlusion (BAO) can cause posterior circulation stroke. There are two predominant therapies for BAO: standard medical treatment (SMT) and SMT plus endovascular thrombectomy (EVT). However, a conclusive systematic comparison of the safety and efficacy of SMT and those of SMT plus EVT for the treatment of BAO is lacking. Thus, a systematic review and meta-analysis is needed to evaluate the safety and efficacy of SMT and SMT plus EVT for the treatment of BAO. This protocol is drafted referring to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses for Protocols guidelines. We will search eligible studies from four main databases including MEDLINE, Web of Science, Cochrane Library and Embase. Randomised controlled trials (RCTs) and observational studies published before 1 October 2020 will be included. Two reviewers in our team will conduct the study selection and data extraction independently. Risk of bias will be assessed by Cochrane Collaboration criteria and the Newcastle-Ottawa scale for RCTs and observational studies, respectively. We will assess the good functional outcomes defining the modified Rankin scale score ≤2 at 90 days after treatment, short-term stroke severity as National Institutes of Health Stroke Scale score at 24 hours after intervention, and successful recanalisation as a modified Thrombolysis in Cerebral Infarction scale score of ≥2b after intervention. Also, safety outcomes will be assessed. The performance of this meta-analysis will depend on the quantity of included studies. The assessment of study heterogeneity will be performed by the I2 statistic. If there is mild heterogeneity (I2<20%) of intervention outcomes in included studies, the fixed-effect model will be applied; otherwise, the random-effect model will be performed. Subgroup analyses and an assessment of publication bias will also be conducted with sufficient data. No collection of primary data from patients is needed. Therefore, the ethical approval is unnecessary. The results may be presented in a peer-reviewed journal and related conferences. CRD42020176764. © Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.