Objective. This study aimed to investigate the incidence and risk factors for musculoskeletal injuries among junior badminton athletes during a national championship. Methods. A retrospective cohort study was conducted among 128 junior badminton athletes who were members of one Indonesian badminton club and participated in the National Premier Circuit held in June 2019 in West Java, Indonesia. Data on demographic characteristics, history of previous and current injuries, physical examination, diagnosis (type, anatomical structure involved, and location), and treatment of injuries were collected along with data on the format of the game (single, double, or combination), and the number of matches for each respective athlete. Measures of injury frequency used were the incidence proportion and clinical incidence. Determinant factors for incidence were investigated. Results. Twenty-four injury events involving 23 athletes were recorded, with an incidence proportion of 23/128 athletes (18%) and a clinical incidence of 24/128 athletes or 18.8 per 100 athletes. Acute injuries were more frequent (13/24, 54.2%) than chronic/overuse injuries. More than half (14/24, 58.3%) of the injuries occurred in the lower extremities. Factors that increased the risk of injury were age ≥ 15 years (relative risk [RR] = 6.26, 95% confidence interval [CI] 1.96, 20.04, p < 0.001), and the number of matches ≥ 3 (RR = 3.79, 95% CI 1.61, 8.92, p = 0.001). Conclusion. Musculoskeletal injuries occurred frequently among Indonesian junior badminton athletes during the national elite championship. An effective injury-prevention program specific to young athletes should be developed to maintain their future participation and performance in competition.