We report a very rare case of Japanese encephalitis (JE) presenting with reversible stereotyped movement in the subacute stage. A 58-year-old woman presented with high fever, headache, nausea, vomiting, and consciousness disturbance. Cranial magnetic resonance imaging (MRI) of fluid attenuated inversion recovery (FLAIR) and T2-weighted image (WI) showed high intensity areas in the bilateral thalamus, caudate nucleus and hippocampus. She developed coma, convulsion, and ballism in the acute stage. One month after onset, she showed rhythmic, stereotyped, repetitive movements with hypoperfusion in the thalamus and frontal cortex on single photon emission computed tomography (SPECT). Three months later, her stereotyped movement improved accompanied by recovery of hypoperfusion in the thalamus and frontal cortex on SPECT. We speculated that her stereotyped movement was clonic perseveration due to frontal dysfunction induced by thalamofrontal disconnection.