Glenohumeral internal rotation deficit (GIRD) and weakness in prone external rotation are risk factors for shoulder and elbow injuries in high school baseball pitchers. While a shoulder-stretching prevention program to improve GIRD decreases the injury rate, the effects of external rotation strength remain unclear. This non-inferiority (NI) study investigates the hypothesis that external rotation strength training is not inferior to sleeper stretching for shoulder and elbow injury prevention in high school baseball pitchers. Participants were randomly allocated to the stretching (n = 62; active control group) and muscle-training (n = 51) groups. Specific exercises were performed each night. Elbow and shoulder injuries were monitored for 150 days. Kaplan–Meier survival curves were generated, and the hazard ratios (HRs) for injury occurrence were calculated using multivariate Cox regression. The log-rank test was used to compare the injury-free time. A one-sided NI test using a fixed NI margin was performed (significance level, P = 0.025). The injury rates were 22.6% (n = 14) in the stretching group and 9.8% (n = 5) in the muscle-training group. The muscle-training group had a lower injury rate (P < 0.001) and a lower risk of injury than the stretching group (HR = 0.489). Therefore, external rotation muscle strength training is not inferior to stretching for preventing baseball-related arm injuries.