This study examined the alterations of heart rate variability (HRV) following iso-duration resistance (RES) and sprint-interval (SIE) exercises by comparing with that of non-exercise control (CON) in 14 non-obese (NOB) and 15 obese (OB) young men. Time and frequency domain measures as well as non-linear metrics of HRV were assessed before and immediately after exercise, and during every 20 min until 120 min post exercise. The variables during the first 4 hrs of actual sleep time at night, and the period of 12-14 hrs post exercise were also measured. All trials were scheduled at 20:00. It was found that RES and SIE attenuated the HRV in both NOB and OB (P <0.05), and the attenuated HRV restored progressively during subsequent recovery. Although the changes in HRV indices among various time points during the recovery period and its interaction across RES, SIE and CON were not different between NOB and OB, the restoration of the declined HRV indices to corresponding CON level in the two exercise trials in OB appeared to be sluggish in relative to NOB. Notwithstanding, post-exercise HRV that recorded during actual sleep at night and during 12-14 hrs apart from exercise were unvaried among the three trials in both groups (P>0.05). These findings suggest that obesity is likely to be a factor hindering the removal of exercise-induced cardiac autonomic disturbance in young men. Nonetheless, the declined HRV following both the RES and SIE protocols were well restored after a resting period of ~10 hrs regardless of obesity. The study was registered at ISRCTN as DOI:10.1186/ISRCTN88544091.