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Introduction: The aim of the present study was to investigate the expression of estrogen-related receptor alpha (ERRα) - an important factor in cellular energy homeostasis regulation - in skeletal muscle of male Wistar rats after four weeks of endurance training and to determine its role with fat metabolism indexes. Methods: In this experimental study, 30 male Wistar rats (eight weeks-old) were randomly divided into four groups: control (n=7), control+XCT790 (n=8), endurance training (n=8), and endurance training+XCT790 (n=7). ERRα was inhibited by intraperitoneal injection of XCT790 (0.48 mg/kg.day) on daily bases. Four weeks of endurance training (five times per week) started at 15 m/min for 20 min and reached to 27 m/min for 50 min was performed by the animals from trained groups. Expression of ERRα, Medium-chain acyl-CoA dehydrogenase (MCAD) and Carnitine Palmitoyl Transferase 1 (CPT-1β) mRNA was measured by Real-Time PCR and quantified by  method. One-way analyses of variance were used for cross-group comparison. Results: The expression of ERRα (P˂0.037), MCAD (P˂0.001), and CPT1β (P˂0.001) mRNA in endurance training group was significantly higher than the control group. The expression of MCAD (P˂0.001) and CPT1β mRNA (P˂0.001) in the endurance training+XCT790 group was significantly lower compared to those values of the endurance training group. Conclusion: In sum, expression of ERRα is a trainable factor and its changes are parallel with the increase in expression of lipid metabolism indexes; so, it could have a direct role in endurance training-induced adaptation in fat metabolism.