This investigation aimed to determine if groupings based upon sum of skinfold thickness (SF) would reflect the differences in heart rate variability (HRV) measured for up to 30-minutes following maximal exercise, and to determine the extent in variation in post-exercise HRV that could be accounted for between the following independent variables: SF, body mass index (BMI) and maximal oxygen consumption (VO2max). SF and BMI measurements were performed on fifty-four men who completed maximal exercise testing to determine VO2max. HRV was evaluated for five-minutes before (Pre), at 0-5 minutes post- (Post1) and 25-30 minutes post-exercise (Post2), and analyzed by frequency domain [high frequency (HF) power, and HF to low frequency power ratio (LF:HF)). Two groups were formed based on being above or below the sample mean value of SF. HF and LF:HF were significantly higher and lower, respectively, at Pre and Post 2 in Group 1 compared to Group 2 (p < 0.05), which remained after controlling for VO2max and BMI. Furthermore, there was a significant trend toward baseline in post-exercise HRV in Group 1 (p < 0.05) but not in Group 2 (p > 0.05). In addition, SF was the only variable to significantly relate to the post-exercise HRV parameters (p < 0.05). The findings of this investigation suggest greater SF is related to a delayed return of HRV toward baseline from maximal exercise. The association between SF and HRV is independent of VO2max and BMI.