Lateral ankle sprains are one of the most common musculoskeletal injuries. Up to 70% of individuals who sustain lateral ankle sprains develop chronic ankle instability (CAI). Exercise therapy is considered an effective treatment for patients with CAI. This meta-analysis investigated the efficacy of exercise therapy in CAI patients by reviewing 15 randomized controlled trials (RCTs) involving 586 participants. Databases including PubMed, EMBASE, Cochrane Library, and Web of Science were searched from inception to September 13, 2024. The Cochrane Risk of Bias Tool was used to assess study quality. Meta-analysis, sensitivity analysis, and publication bias analysis were conducted using RevMan 5.3.0 and Stata 18.0 software. The Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) approach was applied to evaluate the quality of evidence. Main outcomes were assessed using the Foot and Ankle Ability Measure (FAAM) and the Star Excursion Balance Test (SEBT). The results demonstrated that exercise therapy significantly improved FAAM-S (MD = 7.98, CI: 4.11 to 11.86, p < 0.0001, I-2 = 30%). Long-term exercise therapy (over 4 weeks) significantly enhanced FAAM-A (MD = 10.95, CI: 6.60 to 15.29, p < 0.00001, I-2 = 0%) and dynamic balance ability of ankle joint (SBET-A: MD = 4.83, CI: 1.04 to 8.63, p = 0.01, I-2 = 62%; SEBT-PM: MD = 6.93, CI: 2.37 to 11.48, p = 0.003, I-2 = 69%; and SEBT-PL: MD = 8.98, CI: 2.66 to 15.29, p = 0.005, I-2 = 86%). After categorizing by exercise type, the results indicated that strength training was more effective in improving SEBT-PL (MD = 8.15, CI: 6.09 to 10.21, p < 0.00001, I-2 = 0%), joint mobilization was more effective in improving SEBT-A (MD = 7.65, CI: 4.93 to 10.37, p < 0.00001, I-2 = 0%), and proprioceptive training was more effective in improving SEBT-PM (MD = 10.46, CI: 5.27 to 15.65, p < 0.0001, I-2 = 33%). In conclusion, long-term, multifaceted exercise therapy demonstrates superior rehabilitation efficacy for patients with CAI. Personalized treatment plans, informed by SEBT assessment results, should prioritize targeted interventions such as joint mobilization, strength training, or proprioceptive training. This approach holds significant theoretical and practical value for optimizing CAI treatment strategies and enhancing patient outcomes.