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<h4>Objective</h4>This study aims to meta-analyze the impact of high-intensity functional training on athletes' physical fitness and sport-specific performance.<h4>Methods</h4>A systematic search was conducted in five well-known academic databases (PubMed, Scopus, Web of Science, EBSCOhost, and the Cochrane Library) up to July 1, 2023. The literature screening criteria included: (1) studies involving healthy athletes, (2) a HIFT program, (3) an assessment of outcomes related to athletes' physical fitness or sport-specific performance, and (4) the inclusion of randomized controlled trials. The Physical Therapy Evidence Database (PEDro) scale was used to evaluate the quality of studies included in the meta-analysis.<h4>Results</h4>13 medium- and high-quality studies met the inclusion criteria for the systematic review, involving 478 athletes aged between 10 and 24.5 years. The training showed a small to large effect size (ES = 0.414-3.351; all p < 0.05) in improving upper and lower body muscle strength, power, flexibility, and sport-specific performance.<h4>Conclusion</h4>High-intensity functional training effectively improves athletes' muscle strength, power, flexibility, and sport-specific performance but has no significant impact on endurance and agility. Future research is needed to explore the impact of high-intensity functional training on athletes' speed, balance, and technical and tactical performance parameters.