The purpose of this study was to determine the effect of high intensity interval training (HIIT) on heart rate variability (HRV) and aerobic capacity in obese adults with type 2 diabetes mellitus (T2DM).Forty sedentary obese male subjects diagnosed with T2DM were enrolled in the study. Subjects were randomized into two groups. Group A comprising 20 subjects who performed a 12-week HIIT program and group B comprising 20 subjects as a control group maintained their ordinary activities during the intervention period and did not participate in any exercise program. Anthropometric measures, HRV, peak oxygen consumption (VO2peak), glycated hemoglobin (HbA1c), and blood lipids were measured at baseline and at the end of the exercise program. The HIIT included three 30-min sessions per week. Each HIIT session started with 3 minutes warming-up followed by a 4 high intensity (80-90% heart rate max) periods (four minutes each) interspersed with 4 moderate intensity (50-60% heart rate max) recovery intervals (two minutes each) and ended by 3 minutes cooling down. The HIIT program produced statistically significant improvement in HRV parameters (p<0.05) without significant weight reduction. In addition, there were significant improvements in resting heart rate, glycated hemoglobin and total cholesterol (p<0.05). The study also showed that the improvement in the overall HRV was positively correlated with the VO2peak changes. HIIT can be considered as a promising exercise mode for reducing cardiovascular risk factors in obese individuals with T2DM through improving cardiovascular autonomic function and aerobic capacity even in the absence of significant weight reductions.