Objectives This study was performed to investigate whether exercise and quercetin have an effect on muscle energy charge in the metabolic syndrome (MetS) model of rats. Methods Male Sprague-Dawley rats consisting of Control, Fructose, Quercetin, Exercise, Fructose + Exercise, Fructose + Quercetin, Fructose + Quercetin + Exercise groups were randomly divided into seven groups, six rats in each group. Consequently, it was determined that the 20% fructose supplement for 10 weeks with drinking water let to metabolic syndrome in the animals depending on the increase of systolic blood pressure, serum triglyceride, serum insulin and high HOMA-IR scores. MetS criteria were successfully established by oral fructose administration. Results ATP and AMP levels were higher in fructose and exercise groups, and ADP levels were lower. The energy charge increased in quercetin treated groups. We found that regular aerobic exercise and quercetin application might be beneficial in the fructose-mediated MetS in accordance with previous studies. However it was found that quercetin was more effective than exercise in muscle. Conclusions Consequently, it is thought that the regular aerobic exercise alone is a preventive method for the MetS and also it can be used together with quercetin as a beneficial treatment.