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Omega-3 polyunsaturated fatty acids (PUFAs) are known to modulate inflammatory signaling and enhance muscle recovery from exercise-induced stress. In this work, a meta-analysis was conducted that adhered to the PRISMA 2020 criteria, incorporating evidence from 41 randomized controlled trials on eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) supplementation, all of which had been conducted as evidence between 2011 and 2025 and evaluated the effects of EPA and DHA supplementation on the primary markers of the impact of exercise on inflammation and muscle injury, including the random-effects model with moderator dose, intervention duration, sex, and training status. The integrated findings showed that interleukin-6, tumor necrosis factor-α, creatine kinase, and delayed-onset muscle soreness (standardized mean difference = -0.4 to -0.7) were significantly and moderately reduced, indicating a uniform response to omega-3 supplementation's anti-inflammatory and recovery-promoting effects. C-reactive protein responses were more dispersed, suggesting that baseline inflammation differed and that the sampling protocols did as well. Subgroup analyses showed that doses of 2 g/day or more of mixed EPA + DHA, with a minimum duration of 6 weeks of administration, produced the strongest effects, especially among recreational athletes rather than elite athletes. Mechanistically, nuclear factor-kappa B activation and the ensuing synthesis of specialized pro-resolving mediators (resolvins, protectins, and maresins), as well as an increase in cellular antioxidant capacity, appear to be moderated by omega-3 supplementation and support efficient resolution of inflammation and tissue repair. These results form a body of evidence over more than 10 years, showing that omega-3 fatty acids are a strong, evidence-based nutritional tool for reducing the effects of post-exercise inflammation, supporting functional recovery, and sustaining long-term athletic performance.