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The purpose of this study was to analyze effects of yoga exercise on maximal oxygen consumption (VO2max),cortisol level, and creatine kinase myocardial bond activity in female patients with shoulder pain. Subjects comprised 20 female patients with shoulder pain. The subjects were divided into 2 equal groups to ensure biologic homogeneity: the exercise group (n = 10) and non-exercise control group (n = 10). The subjects’ body composition, VO2max, cortisol level, and creatine kinase myocardial bond activity were measured before and after a 12-week yoga exercise program. After the 12-week yoga exercise program, the exercise group demonstrated slightly higher VO2max and creatine kinase myocardial bond activity than the control group, but the differences were not statistically significant. In addition, there was no significant difference in the blood concentration of cortisol between groups. However, in the control group, the cortisol level increased significantly (p < 0.05) after the program, whereas in the exercise group, it decreased significantly (p < 0.05). Our findings indicate that aerobic exercise such as yoga improves body composition, VO2max, cortisol level, and creatine kinase myocardial bond activity in female patients with shoulder pain.