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Background With the continuous advancement of sports training methodologies, high-intensity interval training (HIIT) and small-sided games (SSG) have emerged as crucial strategies for enhancing players’ physical fitness. However, the comparative effects of these training modalities on various fitness components and their underlying physiological adaptation mechanisms remain insufficiently explored. Objectives This systematic review and meta-analysis aim to compare the overall impact of HIIT and SSG on players’ physical fitness and examine the moderating effects of different training parameters, including training frequency, intervention duration, players’ training experience, age, and gender. The findings seek to provide theoretical insights for optimising training protocols. Methods A systematic search was conducted in databases including PubMed, Web of Science, Scopus, and EBSCOhost to identify relevant English-language randomised controlled trials that met predefined eligibility criteria. Hedges’ g was used as the effect size metric, and a random-effects model was applied for meta-analyses of power, speed, endurance, and agility. Subgroup analyses were performed to assess the influence of potential moderators. Results The meta-analysis revealed that, compared to SSG, HIIT produced a small but statistically significant improvement in speed (ES = 0.564) and a moderate and statistically significant improvement in endurance (ES = 0.706). In contrast, gains in power (ES = −0.144) and agility (ES = −0.159) were trivial in magnitude and not statistically significant. Subgroup analyses indicated that lower training frequency (<3 sessions per week) and shorter intervention duration (<6 weeks) yielded significant improvements. Furthermore, players across different age groups benefited from HIIT, while sex did not exhibit a significant moderating effect. Conclusion This systematic review and meta-analysis confirm that both HIIT and SSG effectively enhance players’ physical fitness, with HIIT demonstrating a distinct advantage in improving speed and endurance. Although HIIT showed relatively limited improvements in power and agility compared to SSG, both training modalities exert their effects through distinct physiological adaptation mechanisms. Subgroup analysis findings suggest that appropriately balancing training frequency and intervention duration is crucial for achieving optimal training outcomes. Future research should further investigate the long-term effects of these interventions to provide a more robust theoretical foundation for personalised training program design. Systematic Review Registration https://www.crd.york.ac.uk/prospero/ , identifier CRD42024555633.