Introduction Revascularisation surgery is an important treatment of moyamoya disease (MMD). Several general methods of revascularisation had been used: direct, indirect and combined techniques. However, there had been no reports about the criteria of recipient arteries selection in bypass surgery for MMD. Surgeons usually choose the recipient arteries by their own experiences. Their choices of the recipient arteries are various and may contribute the different outcome of patients. The purpose is to identify utility and efficacy of precision bypass guided by multimodal neuronavigation of MMD in a prospective randomised controlled trial. Method and analysis This study is a prospective randomised controlled clinical trial. This study will enrol a total of 100 eligible patients. These eligible patients will be randomised to the empirical bypass group and the multimodal neuronavigation-guided precision bypass group in a 1: 1 ratio. Patient baseline characteristics and MMD characteristics will be described. In the multimodal neuronavigation-guided group, the blood velocity and blood flow of the recipient arteries will be identified. Surgical complications and outcomes at pretreatment, post-treatment, at discharge and at 3 month, 6 month, 12 month and end of trial will be analysed with CT perfusion, MRI, digital subtraction angiography, modified Rankin Scale, National Institute of Health Stroke Scale and modified Barthel Scale. This trial will determine whether multimodal neuronavigation-guided precision bypass is superior to empirical bypass in patients with MMD and identify the safety and efficacy of multimodal neuronavigation-guided precision bypass. Ethics and dissemination The study protocol and written informed consent were reviewed and approved by the Clinical Research Ethics Committee of Peking University International Hospital. Study findings will be disseminated in the printed media. The study started in August, 2018 and expected to be completed in December, 2020.