Basketball is a major sport worldwide among different age groups that leads to a high frequency of injuries at multiple body sites. Upper and lower extremities and lower back are common pain sites in basketball players; however, there is little information about the relationship between upper or lower extremity pain and lower back pain. This study elucidated the associations between upper extremity (shoulder and elbow) pain and lower back pain (LBP) among young basketball players. We conducted a cross-sectional study using self-reported questionnaires mailed to 25,669 young athletes; the final study population comprised 590 basketball players, and their median age was 13 years (range: 6-15 years). The point prevalence rates of lower back, shoulder, elbow, and upper extremity pain among young basketball players were 12.9% (76/590), 4.6% (27/590), 2.7% (16/590), and 7.1% (42/590), respectively. Multivariate logistic regression analyses revealed that upper extremity pain was significantly associated with LBP (adjusted odds ratio [OR]: 7.86; 95% confidential interval [CI], 3.93-15.72). Shoulder pain was significantly associated with training per week (> 4 days) (adjusted OR: 4.15; 95% CI: 1.29-13.40) and LBP (adjusted OR: 13.77; 95% CI: 5.70-33.24). This study indicates that upper extremity and shoulder pain is associated with LBP among young basketball players. Assessing for lower back pain, as well as elbow and/or shoulder pain, may help prevent severe injuries in young basketball players. In conclusion, parents and coaches should be properly re-educated to help improve lower back, upper extremity, and shoulder pain among young basketball players.