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Background Endovascular treatment (EVT) is safe and effective in treating acute ischaemic stroke due to basilar artery occlusion (AIS-BAO); nonetheless, the impact of intravenous thrombolysis (IVT) on its efficacy remains unclear.Objective To compare the effectiveness and safety of EVT with or without prior IVT in treating AIS-BAO patients within 4.5 hours after stroke onset.Methods and design A multicentre, prospective, randomised, open-label controlled clinical trial with blinded assessment of endpoints. 340 patients will be consecutively randomised to receive IVT plus EVT or direct EVT in a ratio of 1:1 from about 100 hospitals in China. An interim analysis is planned when one-third (114) of the patients have completed the primary endpoint follow-ups. It anticipates that IVT plus EVT demonstrates superiority over direct EVT. If the superiority of IVT plus EVT over direct EVT is less than expected, the sample size may be expanded by up to 20% of the original size. If the efficacy of the two groups is similar, it will shift to a non-inferiority hypothesis, aiming to evaluate whether direct EVT is non-inferior to IVT plus EVT.Outcome The primary endpoint is the proportion of independent neurological function defined as a modified Rankin Scale score of 0 to 2 at 90±14 days after stroke onset.Discussion This trial is expected to provide novel evidence of the superiority or non-inferiority between EVT with or without IVT in the treatment of patients with AIS-BAO.Trial registration NCT05631847 at ClinicalTrials.gov and ChiCTR2300070584 at Chictr.org.cn.