Pitching motion requires whole-body coordination; therefore, poor control of the lower extremities, pelvis and trunk may cause shoulder and elbow injuries. However, few studies have described the relationship between the shoulder joint function and low back injury in high-school baseball pitchers. A total of 128 healthy high school pitchers underwent pre-season medical checkups, where their shoulder range of motion and shoulder strength were measured. The participants completed a self-recorded daily questionnaire regarding the presence of low back pain. Pitchers were divided into injured and non-injured groups. Low back injury was observed in 13 participants (13.4%). In the injured group, horizontal adduction on the dominant shoulder was significantly less than in the non-injured group. A logistic regression analysis showed that horizontal adduction on the dominant side was a significant independent risk factor for low back injury during the season. It is important to recognize that restriction of the shoulder function not only causes shoulder and elbow injuries but can also risk low back injury.