Background and Objectives Chronic inflammation is associated with the development of various diseases, including atherosclerosis and diabetes. The aim of this study was to investigate the effect of longterm selected aerobic exercises on changes in cystatin C and homocysteine in inactive and overweight middle-aged women. Subjects and Methods Thirty non-athlete middle-aged women (mean age: 46.06±6.97 years, weight: 71.82±9.11 kg, height: 156.9±5.24 cm, and body mass index: 29.2±4.11kg/m2) voluntarily participated in this project and were randomly divided into the experimental and control groups The experimental group performed selected aerobic exercises (65-75% of maximum heart rate) for eight weeks. Blood samples were taken before and 24 hours after the completion of the research protocol to measure the levels of cystatin C and homocysteine. Analysis of covariance was used for intergroup comparisons and paired t-test was used for intergroup comparisons. Results The results showed that there was no significant difference between the experimental and control groups in cystatin C (P=0.09) and homocysteine (P=0.07) after eight weeks of selected aerobic exercises. A significant decrease was observed in weight (P=0.001) and body mass index (P=0.002) in the experimental group compared to the control group. Conclusion Overall, the results of the present study showed that although the eight-week activity program improved the body composition of overweight middle-aged women, longer periods of aerobic exercise are required to examine clearer biochemical results.