Autonomic and cardiac dysfunction may occur after vascular brain injury without any evidence of primary heart disease. During acute stroke, autonomic dysfunction, for example, elevated arterial blood pressure, arrhythmia, and ischemic cardiac damage, has been reported, which may hinder the prognosis. Autonomic dysfunction after a stroke may involve the cardiovascular, respiratory, sudomotor, and sexual systems, but the exact mechanism is not fully understood. In this review paper, we will discuss the anatomy and physiology of the autonomic nervous system and discuss the mechanism(s) suggested to cause autonomic dysfunction after stroke. We will further elaborate on the different cerebral regions involved in autonomic dysfunction complications of stroke. Autonomic nervous system modulation is emerging as a new therapeutic target for stroke management. Understanding the pathogenesis and molecular mechanism(s) of parasympathetic and sympathetic dysfunction after stroke will facilitate the implementation of preventive and therapeutic strategies to antagonize the clinical manifestation of autonomic dysfunction and improve the outcome of stroke.