Background Exercise training improves cardiac autonomic function is still debatable in patients with coronary artery bypass grafting (CABG). The aim of the present review is to assess the effect of exercise on CABG patient’s heart rate variability (HRV) and heart rate recovery (HRR) parameters. Main body Databases (PubMed, Web of Science and PEDro) were accessed for systematic search from inception till May 2022. Eleven potential studies were qualitatively analyzed by using PEDro and eight studies were included in the quantitative synthesis. Meta-analysis was conducted by using a random-effect model, inverse-variance approach through which standardized mean differences (SMDs) were estimated. The analysis of pooled data showed that exercise training improved HRV indices of standard deviation of the R–R intervals (SDNN) [SMD 0.44, 95% CI 0.17, 0.71, p = 0.002], square root of the mean squared differences between adjacent R–R intervals (RMSSD) [SMD 0.68, 95% CI 0.28, 1.08, p = 0.0008], high frequency (HF) [SMD 0.58, 95% CI 0.18, 0.98, p = 0.005] and low frequency-to-high frequency (LF/HF) ratio [SMD − 0.34, 95% CI − 0.65, − 0.02, p = 0.03]. Conclusions Exercise training enhances cardiac autonomic function in CABG patients. Owing to the methodological inconsistencies in assessing HRV, the precise effect on autonomic function still remains conflicted. Future high-quality trials are needed focusing on precise methodological approach and incorporation of various types of exercise training interventions will give clarity regarding autonomic adaptations post-exercise training in CABG. Trial registrationCRD42021230270, February 19, 2021.