The purpose of this study was to examine the influence of postexercise parasympathetic modulation, measured by heart rate variability (HRV), on heart rate recovery (HRR) in boys (n = 13, 10.1 ± 0.8 years) and men (n = 13, 23.9 ± 1.5 years) following maximal and submaximal exercise. Subjects completed 10 min of supine rest, followed by graded exercise on a cycle ergometer to maximal effort. On a separate day, subjects exercised at an intensity equivalent to ventilatory threshold. Immediately following both exercise bouts, 1-min HRR was assessed in the supine position. HRV was analyzed under controlled breathing during the final 5 min of rest and recovery in the time and frequency domains and transformed to natural log (ln) values. Boys had a greater 1-min HRR than men following maximal (58 ± 8 vs. 47 ± 11 beats·min−1) and submaximal (59 ± 8 vs. 47 ± 15 beats·min−1) exercise (p < 0.05). Following maximal exercise, boys had greater ln root mean square successive differences in R-R intervals (2.52 ± 0.95 ms), ln standard deviation of NN intervals (3.34 ± 0.57 ms), ln high-frequency power (4.32 ± 2.00 ms2), and ln low-frequency power (4.98 ± 1.17 ms2) than men (1.33 ± 0.37 ms, 2.52 ± 0.24 ms, 1.32 ± 1.06 ms2 and 2.80 ± 0.74 ms2, respectively) (p < 0.05). There were no differences in any HRV variables between groups following submaximal exercise (p > 0.05). In conclusion, it appears that greater parasympathetic modulation accounts for greater HRR following maximal exercise in boys versus men. Although submaximal HRR was greater in boys, parasympathetic responses were similar between groups.