Metabolic syndrome considers a group of disorders that increase the risk of suffering from Noncommunicable Chronic Diseases. In this sense, prevention and treatment have focused on physical activity as an effective method to restore heart rate variability and decrease health risks. This review was objective to describe the behavior of heart rate variability compared to the practice of physical activity in patients with metabolic syndrome. The metabolic syndrome has been related to a sympathetic predominance and a parasympathetic withdrawal that presents a risk of Chronic Non-Communicable Diseases that can be restored with the regular practice of physical activity. Physical activity can restore heart rate variability related to metabolic syndrome, however, other studies are required to try to explain all the conditions to which autonomic balance responds.