Physically inactive adults are prevalent worldwide. This study compared the effects of short-term high-intensity interval training (HIIT) versus moderate-intensity continuous training (MICT) on heart rate variability (HRV) in physically inactive adults as a preliminary study. Thirteen physically inactive male adults (27.5 +/- 3.80 years) were randomly assigned to HIIT (N = 7) or MICT (N = 6). The HIIT program consisted of 20 min of interval training with cycling to rest ratio of 10/50 s at >/=90% HR(peak), while the MICT program consisted of 40 min of continuous cycling at 60(-)75% HR(peak). Both groups completed eight sessions of training within two weeks. Time and frequency domains of HRV were measured for 20 min with Actiwave-Cardio monitor (CamNtech, UK). The number of R-R interval and inter-beat interval (IBI) were significantly improved (p < 0.05) in both HIIT and MICT programs following eight sessions of training. A significant interaction effect for group by time was found in the lnLF/HF ratio (p < 0.05) where it was only improved in the HIIT group from pre- to post-test. The HIIT program is superior to MICT in improving HRV in physically inactive adults. The HIIT program can be applied as a time-efficient program for improving cardiac-autoregulation.