We report the first case of an autoimmune thyroid encephalopathy presenting with multifocal motor status epilepticus. A 37-year-old female patient was admitted with multifocal motor seizures intractable to intravenous status epilepticus treatments, asymmetrical quadriparesis, truncal ataxia and continuous semi-rhythmical jerks. Pathological signal alterations were detected in both precentral cortices in MRI examination. Autoimmune thyroiditis was diagnosed after radiological examinations of the thyroid gland and thyroid function tests. Seizures promptly ceased following intravenous steroid treatment. Immunohistochemistry studies showed mild to moderate neuronal staining with the plasma and CSF samples. Remarkably, autoimmune thyroiditis may present with migrating focal motor status epilepticus. We recommend anti-thyroid antibody screening for multifocal motor status epilepticus cases of unspecified cause.