Background: Multiple arachnoid cysts are very rare within the central nervous system. The cysts will sometimes increase in size with age, lead to the mass effect or cerebrospinal fluid (CSF) flow obstruction, and cause some symptoms, which requires the surgery intervention. Case presentation: A 35-year-old female was admitted to our hospital with some symptoms related to hydrocephalus for 1 month. Brain magnetic resonance imaging (MRI) revealed well-marginated cystic lesions with CSF signal intensity in the ventricular and cistal systems, bilateral temporal lobes, and left occipital lobe. Cine phase-contrast MRI showed the aqueduct of sylvius was blocked by the cyst in the quadrigeminal cist. We employed endoscopic ventriculocystostomy and septostomy to create the communication of the cyst with ventricular and cist system. As a result, the patient’s symptoms were relieved. Conclusions: Endoscopic management can be an effective way for treating intracranial multiple arachnoid cysts, which is the first report of this kind. We hope that this report could help improve the management of intracranial arachnoid cysts with the neuroendoscopic technology.