Introduction: Irisin is a myokine released from a membrane protein FNDC5 and has positive effects on metabolism. The aim of this study was to compare the effect of high intensity endurance training (HIET) and resistance training (RT) on serum irisin and the insulin resistance index in male rats. Materials and Methods: Twenty-four male rats were randomly divided into the high intensity endurance training (HIET), resistance training (RT) and control groups HIET was conducted on a treadmill for 10 weeks, while RT consisted of climbing a ladder carrying a load suspended from the tail. After 10 weeks of training, serum concentration of irisin, glucose and insulin were measured. Results: Irisin serum levels increased significantly following 10 weeks of HIET, compared with RT (P=0.008). Glucose levels (P=0.001) and insulin resistance index (P=0.009) in the HIET group were significantly lower than the RT group and the control group as well (P=0.001). In addition, high intensity endurance training decreased the body weight of the HIET group significantly (P=0.008). Also, Irisin was found to have a significant negative correlation with glucose and insulin resistance index, whereas no significant relationship was seen between irisin and insulin. Conclusion: Compared to resistance training, HIET is more effective in increasing irisin and the decreasing glucose and the insulin resistance index.