Purpose: This study is intended to examine the aquatic exercise on the improvement of muscle atrophy and motor function in an ischemic stroke model induced by middle cerebral artery occlusion. Methods: We used 60 Sprague-Dawely rats which were divided into 4 groups; the subjects were divided into group of 5 rats. Group I was a group of high dose aquatic exercise after inducing ischemic stroke; Group II was a group of low dose aquatic exercise after inducing ischemic stroke; Group III was a control group, Group IV was a sham group without ischemic stroke. Results: Muscle weight of gastrocnemius muscle was significantly difference in Group II compared to Group III on 8 weeks(p<0.05). For the changes in relative muscle weight of gastrocnemius muscle, there was significant increase in Group II compared to Group III on 8 weeks(p<0.05). For neurologic exercise behavior test, Group II generally had the highest score, compared to other groups. The results of behavior test that Group II improved in degeneration and inflammation of muscle fiber and decreased in destruction of nerve cells and cerebral infarction, indicating a similar state of muscle fiber and brain to Group III. Conclusion: Based on these results, aquatic exercise may improve muscle atrophy and contribute to the improvement of motor function.