Purpose The present study was conducted to compare the effects of low volume of high intensity interval training (LVHIIT) and high volume of high intensity interval training (HVHIIT) on heart rate variability (HRV) as a primary outcome measure, and on maximum oxygen consumption (VO2max), body composition, and lower limb muscle strength as secondary outcome measures, in sedentary young women. Methods Thirty-six participants were recruited in this study. The LVHIIT group (n = 17) performed one 4-min bout of treadmill running at 85%-95% maximum heart rate (HRmax), followed by 3 min of recovery by running at 70% HRmax, three times per week for 6 weeks. The HVHIIT group (n = 15) performed four times 4-min bouts of treadmill running at 85%-95% HRmax, interspersed with 3-min of recovery by running at 70% HRmax, 3 times per week for 6 weeks. All criterion measures were measured before and after training in both the groups. Results Due to attrition of four cases, data of 32 participants was used for analysis. A significant increase in high frequency (HF) power (p < 0.001) and decrease in the ratio of low frequency to high frequency power (LF/HF) ratio (p < 0.001) in HRV parameters, was observed post-HVHIIT, whereas, these variables did not change significantly (HF: p = 0.92, LF/HF ratio: p = 0.52) in LVHIIT group. Nevertheless, both the interventions proved equally effective in improving aerobic capacity (VO2max), body composition, and muscle strength. Conclusion The study results suggest that both LVHIIT and HVHIIT are equally effective in improving VO2max, body composition, and muscle strength, in sedentary young women. However, HVHIIT induces parasympathetic dominance as well, as measured by HRV.