Purpose: This study aimed at examining the autonomic cardiovascular modulation in well-trained masters and young cyclists following high-intensity interval training (HIT). Methods: Nine masters (age 55.6 ± 5.0 years) and eight young cyclists (age 25.9 ± 3.0 years) completed a HIT protocol of 6 x 30 sec at 175% of peak power output, with 4.5-min’ rest between efforts. Immediately following HIT, heart rate and R–R intervals were monitored for 30-min during passive supine recovery. Autonomic modulation was examined by i) heart rate recovery in the first 60-sec of recovery (HRR60); ii) the time constant of the 30-min heart rate recovery curve (HRRτ); iii) the time course of the root mean square for successive 30-sec R–R interval (RMSSD30); and iv) time and frequency domain analyses of subsequent 5-min R–R interval segments. Results: No significant between-group differences were observed for HRR60 (P = 0.096) or HRRτ (P = 0.617). However, a significant interaction effect was found for RMSSD30 (P = 0.021), with the master cyclists showing higher RMSSD30 values following HIT. Similar results were observed in the time and frequency domain analyses with significant interaction effects found for the natural logarithm of the RMSSD (P = 0.008), normalised low-frequency power (P = 0.016) and natural logarithm of high-frequency power (P = 0.012). Conclusion: Following high-intensity interval training, master cyclists demonstrated greater post-exercise parasympathetic reactivation compared to young cyclists, indicating that physical training at older ages has significant effects on autonomic function.