This meta-analysis was conducted to investigate the effects of exercise training on heart rate variability (HRV) parameters associated with the autonomic nervous system (ANS) activity. Randomized controlled trials (RCTs) involving healthy adults (aged ≥ 18 years) were included. We searched PubMed, Scopus, Web of Science, and EBSCO databases to identify relevant studies. A random-effects meta-analysis was performed using the standardized mean difference (SMD) and 95% confidence interval (CI). Sixteen RCTs with a total of 623participants were selected for the final analysis. The analysis showed that exercise training improved the standard deviation of normal-to-normal intervals (SDNN) (SMD: 0.58 (0.16, 1.00); p = 0.007), the root mean square of successive differences in heart period series (RMSSD) (SMD: 0.84 (0.36, 1.31); p = 0.0005), and the absolute power of high-frequency band (HF) (SMD: 0.89 (0.27, 1.51); p = 0.005) parameters compared to the control group. Analysis of the moderator variables showed that the effect of exercise on HRV indices may be influenced by sex, age, and type of exercise used, specifically in HF band, absolute power of low-frequency band (LF), and LF/HF ratio parameters. Despite the limited number of existing RCTs related to the subject, the results suggest that exercise training enhances HRV parameters associated with vagal-related activity (RMSSD and HF) and both sympathetic and parasympathetic activities (SDNN). This study overcomes the lack of meta-analyses on the effects of exercise training on autonomic modulation among healthy adults and may bridge the gap in understanding the potential physiological underpinnings of the acknowledged positive health benefits of exercise.