Polycystic ovary syndrome (PCOS) is an endocrine disorder associated with several cardiometabolic risk factors, such as central obesity, insulin resistance, type 2 diabetes, metabolic syndrome, and hypertension. These factors are associated with adrenergic overactivity, which is an important prognostic factor for the development of cardiovascular disorders. Given the common cardiometabolic disturbances occurring in PCOS women, over the last years studies have investigated the cardiac autonomic control of these patients, mainly based on heart rate variability (HRV). Thus, in this review, we will discuss the recent findings of the studies that investigated the HRV of women with PCOS, as well as noninvasive methods of analysis of autonomic control starting from basic indexes related to this methodology.