A 16-year-old girl with a history of Graves’ disease presented with two episodes of generalised tonic-clonic seizures, necessitating intensive care admission. Laboratory examination demonstrated a suppressed thyroid-stimulating hormone level with dramatically elevated free triiodothyronine, free thyroxine and thyroid-stimulating immunoglobulins. Cerebrospinal fluid analysis showed oligoclonal banding in the absence of pleocytosis, thyroid peroxidase antibodies or infection. Neuroimaging revealed the presence of a congenital arachnoid cyst in the right temporal lobe. Despite restoration of euthyroidism and administration of antiepileptic and antiviral drugs, neurological features persisted. Subsequently, intravenous corticoids were administered to exclude the contribution of an underlying autoimmune encephalopathy. The patient gradually recovered and, in retrospect, elevated serum N-methyl-d-aspartic acid-receptor (NMDA-R) antibodies were detected. Although this patient presented with an intracerebral arachnoid cyst that can act epileptogenic per se, the combination of prolonged postictal encephalopathy with unresponsiveness to antiepileptic measures, absence of focal epileptiform activity on EEG, response to corticoids and serum NMDA-R antibody positivity favours the diagnosis of autoimmune NMDA-R encephalitis in this case.