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BACKGROUND Dandy-Walker malformation (DWM) was first reported in 1914. In this case report, a pediatric case was complicated with giant and isolated arachnoid cysts in the right cerebellar hemisphere along with the typical DWM. CASE SUMMARY The patient was at 20 mo old boy, with the complaint of staggering for more than 2 mo. He was admitted to the hospital due to high intracranial pressure and staggering. At admission, the patient had typical manifestations of high intracranial pressure, including vomiting, poor appetite and feeding difficulty. Physical examination revealed increased head circumference, closed anterior fontanelle, unstable standing, staggering, leaning right while walking and ataxia. After admission, he was diagnosed with DWM accompanied by giant isolated arachnoid cysts in the posterior fossa. He underwent Y-shaped three-way valve repair for treating differential pressure between the supratentorial hydrocephalus and the subtentorial arachnoid cysts at once. The child recovered well after the surgery. CONCLUSION In this case, supratentorial and subtentorial shunts were placed, which solved the problem of differential pressure between the supratentorial and subtentorial parts simultaneously. This provides useful information regarding treatment exploration in this rare disease.