INTRODUCTION: Hashimoto encephalopathy is a very rare autoimmune disease of unknown etiology. The spectrum of clinical manifestations is wide, and there is no characteristic presentation. Because of the good response to corticosteroid treatment, it is important to confirm the diagnosis as fast as possible. CASE REPORT: We report an 18-year-old man stroke patient with fever, headache, and neuropsychological symptoms. He presented with clinical, neuroradiologic, and cerebrospinal fluid-findings of cerebral small vessel vasculitis. After extensive investigations and exclusion of other causes of stroke, vasculitis, and collagenosis, we validated the diagnosis of Hashimoto encephalopathy. Treatment with corticosteroids leads to a prompt remission of disease and a good recovery of the patient. CONCLUSIONS: The reported case demonstrates the clinical difficulties in validating a rare cause of stroke in a young patient. Because of the highly effective treatment it is important to consider HE in the differential diagnosis in patients with nonspecific clinical symptoms and MRI findings even when laboratory tests, angiography, and MR-angiography are normal.