Stroke is a major cause of functional disability and is increasing in frequency. Therefore, stroke prognosis must be both accurate and timely. Among other biomarkers, heart rate variability (HRV) is investigated in terms of prognostic accuracy within stroke patients. The literature research of two databases (MEDLINE and Scopus) is performed to trace all relevant studies published within the last decade addressing the potential utility of HRV for stroke prognosis. Only the full-text articles published in English are included. In total, forty-five articles have been traced and are included in the present review. The prognostic value of biomarkers of autonomic dysfunction (AD) in terms of mortality, neurological deterioration, and functional outcome appears to be within the range of known clinical variables, highlighting their utility as prognostic tools. Moreover, they may provide additional information regarding poststroke infections, depression, and cardiac adverse events. AD biomarkers have demonstrated their utility not only in the setting of acute ischemic stroke but also in transient ischemic attack, intracerebral hemorrhage, and traumatic brain injury, thus representing a promising prognostic tool whose clinical application may greatly facilitate individualized stroke care.