We report an 11 year old girl with multi-focal spontaneous myoclonus, generalized seizures and behavioural changes. She was found to have sub-clinical hypothyroidism and elevated anti-thyroid peroxidase antibodies. A diagnosis of Hashimoto encephalopathy (or Steroid Responsive Encephalopathy with Autoimmune Thyroiditis) was made in view of consistent clinical and laboratory features. The patient showed and maintained significant improvement with valproate, clonazepam and long term prednisolone. Other findings included mild cerebral cortical grey matter atrophy on brain magnetic resonance imaging and intermittent slowing with generalized poly-spike-and-wave discharges on electroencephalography. Other causes of progressive myoclonus epilepsy (PME) syndrome including subacute sclerosing panencephalitis, Lafora body disease, Juvenile Neuronal Ceroid Lipofuscinosis, Late onset gangliosidosis, Sialidosis, mitochondrial disorders and coeliac disease were ruled out by appropriate investigations. No other auto-immune abnormality was detected. This case emphasizes that Hashimoto encephalopathy should be considered in the etiologies of PME syndrome in adolescents since it is a treatable entity.