Determining thresholds by measuring blood lactate levels (lactate thresholds) or gas exchange (ventilatory thresholds) that delineate the different exercise intensity domains is crucial for training prescription. This systematic review with meta-analyses aims to assess the overall validity of the first and second heart rate variability - derived threshold (HRVT1 and HRVT2, respectively) by computing global effect sizes for agreement and correlation between HRVTs and reference - lactate and ventilatory (LT-VTs) - thresholds. Furthermore, this review aims to assess the impact of subjects' characteristics, HRV methods, and study protocols on the agreement and correlation between LT-VTs and HRVTs. Systematic computerised searches for studies determining HRVTs during incremental exercise in humans were conducted. The agreements and correlations meta-analyses were conducted using a random-effect model. Causes of heterogeneity were explored by subgroup analysis and meta-regression with subjects' characteristics, incremental exercise protocols, and HRV methods variables. The methodological quality was assessed using QUADAS-2 and STARDHRV tools. The risk of bias was assessed by funnel plots, fail-safe N test, Egger's test of the intercept, and the Begg and Mazumdar rank correlation test. Fifty included studies (1160 subjects) assessed 314 agreements (95 for HRVT1, 219 for HRVT2) and 246 correlations (82 for HRVT1, 164 for HRVT2) between LT-VTs and HRVTs. The standardized mean differences were trivial between HRVT1 and LT1-VT1 (SMD = 0.08, 95% CI -0.04-0.19, n = 22) and between HRVT2 and LT2-VT2 (SMD = -0.06, 95% CI -0.15-0.03, n = 42). The correlations were very strong between HRVT1 and LT1-VT1 (r = 0.85, 95% CI 0.75-0.91, n = 22), and between HRVT2 and LT2-VT2 (r = 0.85, 95% CI 0.80-0.89, n = 41). Moreover, subjects' characteristics, type of ergometer, or initial and incremental workload had no impact on HRVTs determination. HRVTs showed trivial differences and very strong correlations with LT-VTs and might thus serve as surrogates. These results emphasize the usefulness of HRVTs as promising, accessible, and cost-effective means for exercise and clinical prescription purposes.