Heart rate variability (HRV), as a safe and noninvasive marker of autonomic activity, is becoming a prescreening tool for the prediction of cardiovascular complications such as myocardial infarction and heart failure after cerebral stroke. With good reproducibility and quantitative assessment of autonomic nervous system function, the association of some HRV parameters with neurological functional prognosis and stroke recurrence has been widely reported. However, current studies on the relationship between HRV and the clinical outcomes of stroke remain controversial. Previous studies on HRV have mainly focused on stroke prognosis or its role as a clinical biomarker, whereas other roles have rarely been explored. In this article, we review recent advances in the role of HRV in cerebral stroke according to current progress. Specifically, we summarized the role of HRV in the outcomes, complications, treatments, and mechanisms of stroke, based on the latest research. Further, in-depth implications of HRV in stroke are discussed.