Japanese encephalitis (JE) is endemic throughout most of the western Pacific region where Taiwan is located. About half the survivors are left with neurological damages. We report a 55-year-old male who survived from JE and was left with sequela of parkinsonism and severe swallowing disorder. Later, it was proved to be cricopharyngeal dysphagia (CPD) using esophagogram and manometry, which disclosed involuntary hypertonic and hyperreflexic cricopharyngeal muscle contraction. CPD, a life-threatening neurological sequel of JE, has never been reported in the JE survivors before and possibly results from disseminated lesions over pyramidal and extrapyramidal systems.