Background and Aim:Spinal cord injury (SCI) is a condition that causes muscle atrophy and motor disability. An imbalance in mitochondrial dynamics may contribute to motor dysfunction. Considering the effective role of exercise in rehabilitation and the antioxidant effect of MitoQ in neural injury patients, this study aimed to investigate the individual and combined effects of these two treatments on the expression of certain genes involved in mitochondrial fission and fusion pathways in the gastrocnemius muscle of SCI rats Materials and Methods: Thirty adult male rats were randomly divided into five groups: Sham, SCI (injury induced at T11-12 using an aneurysm clip), MitoQ group, swimming exercise group, and swimming combined with MitoQ supplementation group. Treatments began two days after SCI induction and continued for 28 days. At the end of the study, after performing the Basso, Beattie, and Bresnahan (BBB) locomotor test, the gastrocnemius muscle was dissected, and the expression of mitochondrial fission genes (Drp-1, Fis-1) and fusion genes (Mfn-2, Opa-1) was evaluated using Real-time PCR. Data were analyzed with GraphPad Prism 9 software. Results:The results showed that after SCI, motor function significantly decreased compared to the sham group. Treatments (swimming, MitoQ, and the combined therapy) significantly improved motor function, with the best improvement observed in the MitoQ group. Furthermore, the expression of mitochondrial fission and fusion genes in the injury group was markedly increased compared to the control group. Groups receiving only swimming exercise and/or MitoQ supplementation reduced the expression of all four genes significantly (p<0.05). Conclusion: All three interventions successfully attenuated the aberrant expression of key mitochondrial fission and fusion genes, restoring their levels toward those observed in the control group. These findings suggest that the improvements in motor function may be mediated through the restoration of mitochondrial dynamics by reestablishing the equilibrium between fission and fusion processes.