Overweight and obesity have been associated with cardiovascular disease, diabetes mellitus type 2, osteoarthritis, respiratory disorders, cancer, and decline in life expectancy. Cardiac autonomic modulation can be assessed based on Heart Rate Variability (HRV), which is an important marker of cardiovascular risk. High Intensity Interval Training (HIIT) has been developed as an alternative exercise with low volume and expected to help efficiently reduce risk factors associated with the overweight condition. To evaluate the effect of the HIIT exercise program for 4 weeks on HRV in overweight men in Medical Rehabilitation Outpatient Clinic at dr. Soetomo Hospital. This study was conducted from October to December 2020. Eighteen men visited the Medical Rehabilitation Outpatient Clinic at dr. Soetomo Hospital was recruited and randomized into the control and exercise groups. The exercise group performed the HIIT exercise program for 4 weeks and the control group received no intervention. HRV measurement was done before and after the intervention for the exercise group and for the control group was taken before and after 4 weeks of observation. Within-group comparison in the exercise group showed significant increase in RMSSD and SDNN while decrease LF/HF ratio (p = 0.009, p = 0.017, and p = 0.034, respectively). Within-group comparison in the control group showed no significant differences. Between-group comparison at the end of study showed no significant differences. The HIIT exercise program for 4 weeks showed significant increase in RMSSD and SDNN also decrease the LF/HF ratio in overweight/obese men.