A diagnosis of Wernicke's encephalopathy (WE) is difficult. Transient hypotension has been reported as a rare complication of WE. We herein report a case of prolonged hypotension and dysuautonomia associated with WE in a 69-year-old man with underlying alcohol abuse. Without apparent etiology of shock, this patient remained hypotensive for 9 days, requiring a vasopressor, despite daily administration of thiamine 600 mg. Fluctuation of blood pressure caused by postural change and bradycardia in the presence of shock indicated that this patient had dysautonomia. This case hereby proposes a possible association between hypotension, dysautonomia and Wernicke's encephalopathy.