Spinal cord injury (SCI) above T6 is followed by a loss of sympathetic supraspinal control of the heart, disturbing the autonomic balance and increasing cardiovascular risk. Heart rate variability (HRV) is a widely used tool for assessing the cardiac autonomic nervous system and positive adaptations after regular exercise in able-bodied subjects. However, adaptations in SCI subjects are not well known. To compare HRV between able-bodied and SCI subjects and analyze the effects of chronic and acute exercise on HRV in the SCI group. We searched MEDLINE, Embase, Web of Science, SciELO, and Google Scholar databases to July 2016. We selected English and Spanish observational or experimental studies reporting HRV after training or acute exercise in SCI patients. We also included studies comparing HRV in SCI individuals with able-bodied subjects. Animal studies and nontraumatic SCI studies were excluded. We screened 279 articles by title and abstract; of these, we fully reviewed 29 articles. Eighteen articles fulfilled criteria for inclusion in this study. SCI individuals showed lower HRV values in the low frequency band compared to able-bodied subjects. Regular exercise improved HRV in SCI subjects, however time and intensity data were lacking. HRV decreases after an acute bout of exercise on SCI subjects, but recovery kinetics are unknown. HRV is affected following SCI. Able-bodied subjects and SCI individuals have different values of HRV. Acute bouts of exercise change HRV temporarily, and chronic exercise might improve autonomic balance in SCI.