BACKGROUND: Exercise plays an essential role in managing cardiovascular disorders, and high-intensity training (HIT) exercise is a potential, time-effective alternative to traditional aerobic exercise. OBJECTIVES: The objective of this study was to evaluate the effect of HIT program on the time and frequency domains of heart rate variability (HRV) in sports professionals and healthy young adults (18–30 years of age) through a systematic review. METHODS: Physiotherapy Evidence Database (PEDro), PubMed, ScienceDirect, Taylor and Francis Online, and Google Scholar were searched for relevant studies. PEDro scale was used to assess internal validity, exclude risk bias, and assess the methodological quality of studies. RESULTS: A total of 4430 search results were obtained by searching for specific keywords, out of which, only 7 studies met the inclusion criteria after removing all the duplicate articles. Our results showed that HIT programs have significant effect on HRV (root mean square of successive difference [RMSSD], mean difference [MD] =13.35, 95% confidence interval [CI] =1.73, 24.97), high-frequency (HF, MD = 381.7, 95% CI = 321.54, 441.86) power, and low- to high-frequency power (MD = -0.10, CI = -0.73, 0.53) ratio in young adult athletes and healthy young adults. No significant difference was found in other HRV variables. CONCLUSION: HIT is an effective exercise program that can cause improvement in parasympathetic and sympathetic cardiac modulation depending on the duration of the HIT program. HIT program can be given for 2–4 weeks to improve HRV in young adults.