Body pain, often considered as an early sign of injury in young players, warrants thorough study. This study aimed to examine the distribution of badminton-related pain and prevalence in pre-adolescent and adolescent badminton players. Profiles of badminton-related pain were surveyed using a questionnaire among 366 pre-adolescent and adolescent badminton players aged 7–12 years. The distribution of badminton-related pain was described, and the pain incidence was calculated. Proportions of pain per 1000-training-hour exposures were the main outcome measures. The analysis considered various age groups (7–8, 9–10, and 11–12 years) and years of badminton experience (≤2, 2–3, and > 3 years). In total, 554 cases of badminton-related pain were reported. The ankle was the most common site, followed by knee, plantar, shoulder, and lower back. The overall pain rate per 1000-training-hour exposure was 3.06. The 11–12-year-old group showed the highest pain rate, significantly greater than the 7–8-year-old group and the 9–10-year-old group. Additionally, the prevalence of pain exhibited an increasing trend with age. Finally, regardless of the age groups, participants with 2–3 years of badminton experience had the highest pain rate. These findings might help inform targeted interventions to reduce the high prevalence of pain in various body regions across pre-adolescent and adolescent badminton players.