[Purpose] This study evaluated the effects of 12 weeks combined aerobic and resistance exercise on heart rate variability in patients with Type 2 diabetes mellitus. [Subjects and Methods] The subjects were 16 female patients with Type 2 diabetes mellitus selected among the participants of a chronic disease management exercise class at C Region Public Health Center in South Korea. Subjects were randomly assigned to the exercise group (n=8; age, 55.97 ± 7.37) or the control group (n=8; age, 57.53 ± 4.63) The exercise group performed aerobic and resistance exercises for 60 minutes per day, 3 times per week for 12 weeks. Anthropometric measurements, biochemical markers, physical fitness, and heart rate variability were examined. [Results] After 12 weeks of exercise, weight, body fat percentage, waist circumference, blood glucose, insulin resistance, glycated hemoglobin level, systolic blood pressure, and diastolic blood pressure significantly decreased and cardiorespiratory fitness and muscular strength significantly increased in the exercise group. Although heart rate variability measures showed favorable changes with the exercise program, none were significant. [Conclusion] Although the exercise program did not show notable changes in heart rate variability in patients with Type 2 diabetes within the timeframe of the study, exercise may contribute to the prevention and control of cardiovascular autonomic neuropathy.