Secondary autoimmune disorders are a recognised complication of alemtuzumab treatment for multiple sclerosis. We report a case of autoimmune encephalitis manifesting as a polymorphic epilepsia partialis continua / status epilepticus seven months after the second course of alemtuzumab in a patient with previous autoimmune hypothyroidism and immune thrombocytopenic purpura. An MRI revealed multifocal cortical abnormalities and neuronal loss was evident on biopsy. Although testing for anti-neuronal antibodies was negative, the patient responded well to immunotherapy including plasma exchange. This is the first reported presentation of an autoimmune encephalopathy secondary to alemtuzumab therapy.