Background and Purpose: Musculoskeletal pain is a major occupational hazard in taekwondo that can negatively affect performance and athletic longevity. However, comprehensive data on the prevalence and pattern of these disorders particularly with respect to laterality (right vs. left) and sex among Iranian athletes are limited. Therefore, this study aimed to determine the prevalence of upper and lower extremity musculoskeletal pain in competitive taekwondo athletes in the city of Arak. Methods: In this descriptive cross-sectional study, 150 taekwondo athletes (115 males, 35 females) aged 8–25 years with at least one year of training experience were selected from clubs in Arak using a convenience sampling method. Data were collected using a demographic questionnaire and the modified Nordic Musculoskeletal Questionnaire (NMQ), which assessed pain in specific joints (shoulder, elbow, wrist, hip, knee, ankle, neck, upper back, and low back) during the past 7 days and past 12 months. Current pain intensity was measured using the Visual Analog Scale (VAS). Data analysis was performed using SPSS software through descriptive statistics (frequency, percentage, mean, standard deviation) and inferential tests (Chi-square and independent t-test). Results: The findings indicated a substantial burden of musculoskeletal pain. The highest 12-month prevalence was observed in the right knee (64%), followed by the low back (60%), right ankle (50%), and right shoulder (45.2%). A clear right-side dominance pattern was observed in the upper extremity and ankle. The distribution of pain during the past 7 days was similar, with the right knee (40%) and low back (30%) being most affected. For most joints, no statistically significant difference in pain prevalence was found between male and female athletes (p > 0.05). However, previous injury was the strongest and most significant predictor of pain in all body regions (p < 0.001). Advanced skill level (belt rank) and higher training frequency were also significantly associated with greater pain prevalence. Conclusion: Musculoskeletal pain—particularly in the knee, low back, ankle, and shoulder—is highly prevalent among taekwondo athletes in Arak, with a clear right-side predominance. Although sex had no significant effect on prevalence, training-exposure factors (skill level, training frequency) and prior injury were key risk factors. These findings emphasize the urgent need for targeted, evidence-based injury-prevention programs, mandatory full rehabilitation protocols after injury, and integration of training load management strategies into practice programs to maintain athlete health and ensure sustainable sport participation.