Introduction: Ankle sprain is one of the most common injuries among the athletes. According to some research, balance deficit and ankle instability are reported in those with chronic ankle instability. The aim of this study was studying the effect of 6 weeks' new balance training in the land and water on balance, instability index and pain in the athletes with chronic ankle instability. Methods: In this semi-experimental study, 30 athletes with chronic ankle instability were selected with purposeful sampling and randomly were placed in two groups (aquatic and land therapy). Pain, instability, the static and semi-static balance were measured pre and post training. The intervention included the sixweek modern balance training in the water and land. To analyze the data, SPSS (22) software was used. to compare the results of the pre-test and post-test, paired sample t-test and to compare the means between two groups, the independent sample t-test was used. The significance level was 0. 05. Results: The results showed that both experimental groups had a significant difference in the instability index (P=0. 001), static (P=0. 001) and semi-dynamic (P=0. 002) balance compared to the pre-intervention stage, but there was no significant difference in pain variable (P=0. 38). However, comparison of the means of the studied variables between the two groups did not show a significant difference in the instability index (P=0. 1), static (P=0. 8, P=0. 6), semi-dynamic (P=0. 9, P=0. 5) and pain (P=0. 8). Conclusion: Many clinicians propose water-based exercises in the ankle injured athletes, which are costly in addition to time-consuming. The results of this study suggest that the patients with chronic ankle instability can rehabilitate by use of available tools, even at home.