Investigations into the sensitivity of heart rate‐(HR) derived indices for tracking parasympathetic nervous system (PNS) changes in functionally overreached (F‐OR) endurance‐trained athletes have produced equivocal findings. Lack of clarity may be a result of methodological inconsistencies. Therefore, the aims of this systematic review and meta‐analysis were (a) to determine the sensitivity of resting and post‐exercise vagal‐related HR variability (HRV) and HR recovery (HRR) indices to detect PNS modulation in F‐OR and non‐overreached (non‐OR) athletes, and (b) to investigate the influence of methodological factors on the sensitivity of HR‐based indices to detect PNS hyperactivity in F‐OR athletes. We searched CENTRAL, Scopus, PubMed, Embase, and Web of Science up to May 2020 for the following terms: male and female endurance‐trained athletes, controlled and uncontrolled studies that carried out an overload training period, and PNS modulation measured in resting and post‐exercise, pre‐ and post‐overload training period. A random‐effects model of standardized mean difference (SMD) was estimated for each outcome measure based on the training‐induced fatigue status (F‐OR vs non‐OR athletes), and the influence of methodological issues to detect PNS hyperactivity in F‐OR was assessed by subgroup analyses. Pooled analysis showed that resting vagal‐related HRV indices did not detect PNS hyperactivity in F‐OR athletes (SMD+ = −0.01; 95% confidence interval CI = −0.51, 0.50), and no statistical difference (P = .600) was found with non‐OR athletes (SMD+ = 0.15; 95% CI = −0.14, 0.45). However, subgroup analysis based on HRV parameter showed a moderate statistical increase in weekly averaged HRV in F‐OR athletes (SMD+ = 0.81; 95% CI = 0.35, 1.26), while isolated HRV values did not reach statistical significance (SMD+ = −0.45; 95% CI = −0.96, 0.06). We observed a moderate and statistically significant increase in HRR indices among F‐OR athletes (SMD+ = 0.65; 95% CI = 0.44, 0.87), no changes for non‐OR athletes (SMD+ = 0.10; 95% CI = −0.15, 0.34), and statistically significant differences between F‐OR and non‐OR athletes (P < .001). Insufficient data prevented meta‐analysis for post‐exercise vagal‐related HRV indices. Our findings show that when methodological factors are considered, HR‐based indices are sensitive to increased PNS modulation in F‐OR.