Dengue is the leading cause of mosquito-borne viral infection. It is responsible for high morbidity and mortality in children living in endemic areas. Nowadays, neurological complications are progressively referred to and include a broad spectrum of symptoms. It can be secondary to metabolic alterations, direct invasion by the virus, and enhanced autoimmune response. Here, we report a rare case of hydrocephalus secondary to dengue encephalitis. A 13-day-old boy was diagnosed with dengue. He evolved with seizures and impaired consciousness being diagnosed with encephalitis. After clinical treatment, he was discharged fully recovered. Three months later, he presented with signs and symptoms of intracranial hypertension. Brain MRI revealed hydrocephalus secondary to acquired aqueduct stenosis. The patient underwent an endoscopic third ventriculocisternostomy. Dengue infection is a differential diagnosis for acute febrile neurological impairment in children from endemic areas. Follow-up should be offered after dengue encephalitis to detect possible late-onset complications, as hydrocephalus.