[Purpose] This study analyzed the effects of yoga exercise on maximum oxygen uptake, cortisol level, and creatine kinase myocardial bond activity in female patients with skeletal muscle pain syndrome. [Subjects] The subjects were 24 female patients with skeletal muscle pain syndrome. [Methods] The subjects were divided into 2 groups: a yoga exercise group (n = 12) and a non-exercise control group (n = 12). Body composition, maximum oxygen uptake, cortisol level, and creatine kinase myocardial bond activity were measured before and after a 12-week yoga exercise program. [Results] After the 12-week yoga exercise program, the exercise group exhibited slightly higher maximum oxygen uptake and creatine kinase myocardial bond activity than the control group, but the differences were not statistically significant. In addition, the exercise group exhibited a significant decrease in cortisol level. [Conclusion] Regular and continuous aerobic exercise such as yoga improves body composition, maximum oxygen uptake, cortisol level, and creatine kinase myocardial bond activity in female patients with skeletal muscle pain syndrome.