Introduction: The high-intensity interval training (HIIT) has been emerged as an alternative method to promote greater adherence of patients, undergoing to cardiovascular rehabilitation programs, since it covers shorter training sessions when compared to conventional continuous training of moderate intensity. However, little is known about the effect of this training modality on cardiac autonomic control, as well as its application in the rehabilitation or prevention of pathologies that present autonomic imbalance as clinical characteristics. Purpose: To conduct a systematic review to evaluate the effects of HIIT on cardiac autonomic control in humans, evaluated by heart rate variability (HRV). Methods: The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement was followed to conducted and reported this review. Electronic databases PEDro, SCOPUS and PubMed were searched from the inception to March 29th, 2018. The eligibility criteria were determined using the Patient/Population, Intervention, Comparison/Comparator, Outcome (PICO) format. Thus, the selected studies had looked at: adults with or without cardiovascular disease (P); who carried out a HIIT program (I); comparisons with other interventions was not included in this systematic review (C); our results of interest were measurements of cardiac autonomic control through HRV indexes (O). Moreover, the PEDro scale was applied to verify the methodological quality from all eligible clinical trials. Finally, data were reported through descriptive analysis and complementary the deltas of HRV indexes (post minus pre) were calculated. Results: The initial search strategy resulted in 339 citations and 2 additional citations were identified through other sources. After the screening and deleting of the duplicate articles, 6 randomized clinical trials were included. The mean score of PEDro was 6 (ranging from 5 to 8), with 3 studies of high and 3 studies of low methodological quality. Overall, the results showed an improvement in parasympathetic and/or sympathetic modulation after HIIT, when evaluated by linear and non-linear indexes of HRV. Conclusion: In according to current state of the art, the HIIT seems to be a promisor method to improve the cardiac autonomic control, especially in healthy individuals and patients with metabolic syndrome, considering the risk of bias of the included studies.