Background: The aim of this study was to evaluate the changes in regional cerebral blood flow (rCBF) in multiple cases of Hashimoto's encephalopathy (HE). Methods: Seven untreated patients with HE and 10 age-matched healthy controls underwent brain single photon emission computed tomography (SPECT) with N-isopropyl-p-[123I]iodoamphetamine. All patients had anti-NH2-terminal of α-enolase autoantibodies (Abs), which served as a useful diagnostic marker for HE, in addition to anti-thyroid Abs in their sera and responded to corticosteroid therapy. The obtained SPECT images were compared between the patients and the controls using 3D-SSP analysis. Results: The rCBF of all patients with HE was significantly decreased in the bilateral anterior cingulate areas and left prefrontal cortex compared with the controls (p < 0.05). Focusing on the HE patients with acute neuropsychiatric symptoms (n = 5) such as consciousness disturbance and/or psychosis, the decreased rCBF in these areas was more significant, and the rCBF in the right frontal cortex was also decreased. Conclusion: Statistical analysis of these multiple-case SPECT images revealed the regions of decreased CBF associated with clinical symptoms, especially acute neuropsychiatric symptoms, in HE patients. This study shed light on the pathophysiological decrease in rCBF observed in HE.