This study determined the reliability of post-exercise heart rate recovery (HRR) and vagal-related HR variability (HRV) after repeated-sprints (RSs), and contrasted it with the smallest worthwhile change (SWC) of these indices. Fourteen healthy male participants performed on four occasions, separated by 7 days, five 30-m sprints interspersed by 25-s of recovery. Post-exercise HR during 10 min of seated rest was measured. HRR during the first 60-s of recovery was computed (HRR60s). HRV indices were calculated in time and frequency domains during the last 5-min of the recovery. Absolute and relative reliability were assessed by typical error of measurement expressed as coefficient of variation (CV) and intraclass correlation coefficients (ICCs), respectively. Sensitivity was assessed comparing SWC to the typical error of measurement. CV ranged from 3.6% to 13.5% and from 6.3% to 109.2% for the HRR and HRV indices, respectively. ICCs were from 0.78 to 0.96 and from 0.76 to 0.92, respectively. HRR and HRV indices showed large discrepancies reliability. HRR60s and the square root of the mean sum of the squared differences between R-R intervals presented the highest levels of both absolute and relative reliability. However, SWC was lower than the typical error of measurement, indicating insufficient sensitivity to confidently detect small, but meaningful, changes in HRR and HRV indices.