Stroke is one of the leading causes of mortality and disability worldwide. Autonomic dysfunction after ischemic stroke is frequently associated with cardiac complications and high mortality. The brain-heart axis is a good model for understanding autonomic interaction between the autonomic central network and the cardiovascular system. Heart rate variability (HRV) analysis is a non-invasive approach for understanding cardiac autonomic regulation. In stroke patients, HRV parameters are altered in the acute and chronic stages of the disease, having a prognostic value. In this literature review we summarize the main concepts about the autonomic nervous system and HRV as autonomic biomarkers in ischemic stroke.