ABSTRACT Anti-N-methyl-D-aspartate (NMDA) receptor encephalitis is a rare and severe autoimmune encephalitis that displays neuropsychiatric symptoms and autonomic instability, e.g., hypoventilation and cardiac arrhythmia. Severe arrhythmia including asystole associated with this encephalitis is rare. Several causes have been suggested. Nevertheless, no report of the literature has described examination by functional brain imaging of a patient with asystole during anti-NMDA receptor encephalitis. This case is that of a 34-year-old woman diagnosed as having anti-NMDA receptor encephalitis. She repeatedly showed 10–20 s asystole episodes necessitating a temporary transvenous pacemaker. After resection of the bilateral ovarian cystic tumor, her symptoms improved. Regional cerebral blood flow (rCBF) was evaluated using single-photon emission computed tomography. The rCBF was increased in the amygdala, hypothalamus, anterior cingulate, hippocampus, and anterior temporal lobes, but decreased in the dorsolateral frontal lobes, parietal lobes, and occipital lobes. Findings in this case suggest that altered rCBF in the patient with asystole episodes associated with anti-NMDA receptor encephalitis was observed in several brain lesions. The rCBF increases in the central autonomic networks, i.e., the amygdala, hypothalamus, and anterior cingulate, might be associated with dysregulation of sympathetic and parasympathetic nervous systems leading to asystole.