Purpose: The aim of the systematic review and meta-analysis was to investigate the effect of various exercise training interventions on cardiac autonomic function (CAF) in obese. Methods: We conducted electronic database search from SCOPUS, PubMed, Web of science and cochrane library from inception till August 2021. Among 3234 articles retrieved, 9 were found to be eligible for the present review. Studies investigating the effect of exercise interventions on CAF assessed either by linear or non-linear measures of heart rate variability (HRV), baroreflex sensitivity, or heart rate recovery were included. Of the studies retrieved, 9 were included in the systematic review. Meta-analysis was conducted on 5 studies. Results: The findings of the qualitative analysis revealed low to moderate certainty of evidence for aerobic exercise (AE) while low to very low was documented for combined training (CT). Standardized mean differences (SMD) showed a large effect of AE on SD of normal to normal (N–N) intervals (SDNN) [SMD 1.35, 95% confidence interval (CI) −0.11, 2.81; p = 0.07] and root mean square of successive differences between adjacent inter-beat (R-R) intervals (RMSSD) [SMD 1.50, 95% confidence interval (CI) 0.12, 2.88; p = 0.03]. CT depicted moderate insignificant change in low-frequency power of HRV (LF; SMD −0.55, 95% CI −1.52, −0.42; p = 0.27). Conclusion: This systematic analysis revealed positive effect of exercise training on CAF in obese individuals. AE and CT have large and moderate impact on CAF respectively though the pooled result was insignificant for majority of the variables, while effect of HIIT and RT yet remains to be fully elucidated.