Background: Performance-related musculoskeletal disorders (PRMD) are highly prevalent among flutists, largely due to the instrument’s markedly asymmetrical posture and sustained upper-extremity loading. Prior research consistently shows localized pain in the neck, thoracic paraspinal, shoulders, wrists, and hands, underscoring the need for flute specific epidemiologic data to better characterize this elevated musculoskeletal risk. Objects: This study examined their associations with performance-related parameters and PRMD to inform evidence-based preventive and rehabilitative strategies in elite female flutists. Methods: This cross-sectional study investigated 35 professional female flutists using a structured questionnaire that assessed performance characteristics, upper extremity function, and regional musculoskeletal symptoms. Group comparisons of pain intensity were examined by t-tests and one-way ANOVA. Results: Flutists showed the greatest pain intensity in both side of upper trapezius, whereas most other regions demonstrated minimal pain. Late starters exhibited significantly higher pain in major upper-body regions, including the upper trapezius, rhomboids. Longer professional career duration was associated with higher pain intensity in the left upper trapezius, left lateral elbow, and mid-lumbar region (all p < 0.05), but not in other body sites (all p > 0.05). Conclusion: This study demonstrated that elite female flutists exhibit a pronounced concentration of PRMD in shoulder regions especially, the upper trapezius of elite female flutists and stated that later initiation of flute training and longer professional career duration significantly increased pain intensity across multiple upper-body sites. These findings indicate that PRMD risk is primarily driven by the interaction between asymmetric postural demands and cumulative occupational load, emphasizing the importance of early posture focused training and targeted preventive strategies.