BackgroundHeparin anticoagulation therapy is a widely used method to prevent cerebral vasospasm (CV) and venous thrombosis in patients with subarachnoid hemorrhage caused by ruptured cerebral aneurysms. Subcutaneous heparin injection is considered safe and effective, whereas continuous intravenous heparin infusion is still being debated due to the risk of bleeding. Although most retrospective studies have confirmed the safety and effectiveness of unfractionated heparin (UFH) after aneurysm embolization therapy and its ability to reduce CV, there is still no randomized clinical trial comparing UFH and subcutaneous low-molecular-weight heparin (LMWH) injection in this population. Therefore, this study aims to compare the clinical outcomes associated with these two treatment approaches.MethodsThe study is an open-label, single-center, randomized controlled trial and aims to recruit 456 patients, with 228 patients in each group. The primary outcome was CV; the second outcomes measures are occurrence of bleeding events, ischemic events, heparin-induced thrombocytopenia, deep vein thrombosis, cerebral venous circulation time, brain edema score, and hydrocephalus incidence.Ethics and disseminationThis study protocol obtained ethical approval from the Ethics Committee of Baoan People’s Hospital, Shenzhen, Guangdong (approval number: BYL20220805). This work will be published in peer-reviewed international medical journals and presented at medical conferences.Trial registrationClinicalTrials ID: NCT05696639. Registered on March 30, 2023.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13063-023-07493-9.