PURPOSE: This systematic review with meta-analysis was conducted to establish whether heart rate variability (HRV)-guided training enhances cardiac-vagal modulation, aerobic fitness, or endurance performance to a greater extent than predefined training while accounting for methodological factors. METHODS: We searched Web of Science Core Collection, Pubmed, and Embase databases up to October 2020. A random-effects model of standardized mean difference (SMD) was estimated for each outcome measure. Chi-square and the I(2) index were used to evaluate the degree of homogeneity. RESULTS: Accounting for methodological factors, HRV-guided training was superior for enhancing vagal-related HRV indices (SMD(+) = 0.50 (95% confidence interval (CI) = 0.09, 0.91)), but not resting HR (SMD(+) = 0.04 (95% CI = -0.34, 0.43)). Consistently small but non-significant (p > 0.05) SMDs in favor of HRV-guided training were observed for enhancing maximal aerobic capacity (SMD(+) = 0.20 (95% CI = -0.07, 0.47)), aerobic capacity at second ventilatory threshold (SMD(+) = 0.26 (95% CI = -0.05, 0.57)), and endurance performance (SMD(+) = 0.20 (95% CI = -0.09, 0.48)), versus predefined training. No heterogeneity was found for any of the analyzed aerobic fitness and endurance performance outcomes. CONCLUSION: Best methodological practices pertaining to HRV index selection, recording position, and approaches for establishing baseline reference values and daily changes (i.e., fixed or rolling HRV averages) require further study. HRV-guided training may be more effective than predefined training for maintaining and improving vagal-mediated HRV, with less likelihood of negative responses. However, if HRV-guided training is superior to predefined training for producing group-level improvements in fitness and performance, current data suggest it is only by a small margin.