Background <p>Varicella-zoster virus infection is typically self-limited in children but can rarely lead to severe neurological and thrombotic complications. Post-infectious immune dysregulation may contribute to conditions such as cerebral venous sinus thrombosis (CVST) and autoimmune encephalitis. Reports describing the coexistence of these complications, particularly with anti-GAD65 antibodies, are exceedingly rare.</p> Case presentation <p>An 8-year-old boy developed seizures, headache, and right-sided hemiplegia twelve days after varicella infection. Neuroimaging revealed CVST with intracranial hemorrhage and cerebral edema, necessitating anticoagulation and decompressive craniectomy. Laboratory findings showed acquired protein S deficiency, suggesting a transient prothrombotic state. His course was complicated by deep vein thrombosis, cytopenias, and epidural abscess requiring antibiotics and surgical intervention. Despite initial stabilization, he developed progressive decline in consciousness and recurrent seizures. Brain MRI demonstrated multifocal T2 hyperintensities, and cerebrospinal fluid analysis showed lymphocytic pleocytosis. Markedly elevated anti-GAD65 antibodies were detected in both serum and CSF, confirming autoimmune encephalitis after exclusion of alternative etiologies. Treatment with high-dose corticosteroids followed by intravenous immunoglobulin resulted in rapid neurological improvement. The patient was discharged with mild residual deficits and showed near-complete recovery on follow-up.</p> Conclusions <p>This case highlights a rare overlap of CVST and anti-GAD65 autoimmune encephalitis following varicella infection, emphasizing the role of infection-triggered immune and coagulation disturbances. Early recognition of evolving neurological symptoms and comprehensive evaluation for autoimmune mechanisms are critical. Prompt immunomodulatory therapy, alongside multidisciplinary management, can significantly improve outcomes in complex post-infectious neurological syndromes.</p>