Exercise-induced muscle damage (EIMD) represents a well-established physiological response to strenuous or unaccustomed physical activity, particularly involving eccentric muscle contractions. It is characterized by microstructural disruption of muscle fibers, increased sarcolemmal permeability, inflammatory activation, oxidative stress, and transient impairment in muscle performance. Understanding these processes is essential for optimizing recovery strategies, preventing overtraining, and enhancing athletic performance. The present study aims to systematically review and quantitatively synthesize evidence on biochemical and molecular biomarkers associated with EIMD and recovery. A comprehensive literature search was conducted across PubMed, Scopus, and Web of Science databases for studies published between 2000 and 2025. Eligible studies included human participants and reported biochemical markers of muscle damage following exercise. A total of 45 studies met the inclusion criteria. Meta-analysis was performed using a random-effects model, with standardized mean difference (SMD) used to quantify effect sizes. The findings indicate that creatine kinase (CK) demonstrated a large effect size (SMD = 1.25), whereas inflammatory markers such as interleukin-6 (IL-6) and oxidative stress markers such as malondialdehyde (MDA) showed moderate effect sizes (SMD = 0.85 and 0.72, respectively). Considerable heterogeneity was observed (I² = 65–80%), reflecting variations in exercise protocols and participant characteristics.