Pain is common in athletes which should be well managed. To identify risk factors for shoulder pain, and the association between shoulder pain, lower back pain and knee pain among elementary school-aged badminton players, we conducted a cross-sectional study to collect data of the past year among 611 elementary school age (7-12 years old) badminton players belonging to the Japan Schoolchildren Badminton Federation using a questionnaire. Odds ratio (OR) and 95% confidence interval (CI) were estimated by multivariate logistic regression analysis. The overall incidence rate of shoulder injuries, lower back injuries and knee injuries was 0.38 injuries per 1000 h of badminton training. Players with training time per day > 2.5 h were 2.64 times (95% CI 1.03-6.78, p = 0.043) more likely to sustain shoulder pain than those with training time per day ≤ 2.5 h. A significant association was revealed between shoulder pain and knee pain as well as between lower back pain and knee pain as training hours per day > 2.5 h. Moreover, lower back pain was significantly associated with shoulder pain independent of training hours per day (≤ 2.5 h: p = 0.001; > 2.5 h: p < 0.001). These findings indicate that training time per day is risk factor, and shoulder pain, lower back pain and knee pain were associated with each other in elementary school-aged badminton players.