Background and aims: Hypothyroidism leads to a reduction in muscle volume and mass. Meanwhile, the myostatin and follistatin genes play a pivotal role in regulating muscle growth, homeostasis, and preventing atrophy. This study investigated the expression of these genes in response to a moderate-intensity exercise program in rats with hypothyroidism. Methods: In this controlled experimental study, 21 male Wistar rats (8 weeks old, weighing 210 ± 15 g) were induced with hypothyroidism (150 mg/kg) and randomly divided into three groups: healthy, hypothyroidism control, and hypothyroidism + endurance training. The intervention group underwent a 6-week endurance training program (speed: 10–20 m/min, duration: 20–40 min). After training and anesthesia, tissue samples were collected, and gene expression was measured using Real-Time PCR. Data were analyzed using a one-way ANOVA test (significance level: p < 0.05) and GraphPad software. Results: Hypothyroidism induction significantly increased myostatin levels (p < 0.0001) and also decreased follistatin levels (p = 0.353) in rats. However, endurance training significantly reduced myostatin (p < 0.0001) and increased follistatin levels (p = 0.01) in hypothyroid rats. Conclusion: Endurance training appears to counteract muscle atrophy and wasting in hypothyroid rats by inducing beneficial changes in the expression of the studied genes.