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We here report a 39-year-old women with an ischaemic encephalopathy in temporal association with the first diagnosis of an essential thrombocythaemia.Diagnosis was difficult due to cognitive impairment, a long lasting period of progressive symptoms, a former febrile infection, relevant weight loss and ambiguous findings in brain imaging. Meningeal and brain biopsy obtained the diagnosis of an ischaemic encephalopathy and reliably delineated this finding from an infectious or malignant disease of the brain. According to the persistent thrombocytosis subsequent bone marrow biopsy revealed a JAK-2 positive essential thrombocytosis. In the absence of any other pathology we suspected a subacute cortical vein thrombosis as the most likely cause of the ischaemic encephalopathy triggered by the underlying essential thrombocythaemia. After initial anticoagulation she was therefore treated with aspirin for prophylaxis of further vascular events and hydroxyurea for cytoreduction. Follow up examination revealed good recovery from neurological symptoms.