Supramaximal interval exercise alters measures of autonomic modulation, while a cool-down may speed the recovery of vagal modulation. The purpose of this study was to compare the effects of a cool-down (pedaling a cycle ergometer at 50 rpm against a resistance of 45 W) versus passive recovery (no pedaling) after supramaximal interval exercise on autonomic modulation. Sixteen moderately active individuals (Mean ± SD: 23 ± 3 years (men: n = 10; women: n = 6) were assessed for autonomic modulation at Rest, and 15 (R15), 30 (R30), 45 (R45) and 60 (R60) min following supramaximal interval exercise. Linear measures of autonomic modulation included natural log (ln) total power (lnTP), high-frequency power (lnHF), the ratio of low frequency (LF) to HF ln(LF/HF) ratio, root mean square of successive differences between normal heartbeats (lnRMSSD), while non-linear measures included sample entropy (SampEn) and Lempel–Ziv entropy (LZEn). Two-way repeated ANOVAs were used to evaluate the main effects of condition (cool-down, passive recovery) across time (Rest, and R15, R30, R45 and R60). There were significant (p ≤ 0.05) condition by time interactions for SampEn and LZEn, such that they decreased at 15, 30, 45 and 60 min during passive recovery compared to Rest, with the recovery of SampEn and LZEn by 60 and 45 min, respectively, during cool-down. There were significant (p ≤ 0.05) main effects of time for lnTP, lnHF and lnRMSSD, such that lnTP, lnHF and lnRMSSD were attenuated, and lnLF/HF ratio was augmented, at all recovery times compared to Rest. These data demonstrate that a cool-down increases the recovery of nonlinear measures of vagal modulation within 45–60 min after supramaximal interval exercise, compared to passive recovery in moderately active individuals.