The current literature offers limited evidence supporting sport-specific plyometric rehabilitation for young throwing athletes. The purposes of this case report were to 1) describe the focused differential diagnosis of a young throwing athlete with shoulder pain and 2) use previously validated, region-specific, health-related quality of life measures to describe clinical outcomes for a rehabilitation program that included sport-specific, plyometric training. The 13-year-old male patient presented in this case report experienced a sudden onset of right shoulder pain while pitching in a baseball game. On physical examination, this patient demonstrated shoulder pain, pain with palpation of the infraspinatus and teres minor muscles, decreased strength of the infraspinatus and teres minor with resultant impaired rotator cuff performance, and signs consistent with anterior shoulder instability. Early rehabilitation consisted of modalities for pain relief and therapeutic exercises to improve strength. In the return to sport phase of rehabilitation, the patient performed sport-specific plyometric exercises that were progressed in difficulty based on the patient's report of pain and muscle soreness. Health-related quality of life was assessed by using the Shoulder Pain and Disability Index (SPADI) and the sports module of the Disability of Arm, Shoulder and Hand (DASH) questionnaires. A standard error of measurement (SEM)-based criterion was used to determine if the patient demonstrated meaningful changes in outcome measures. The patient did not demonstrate meaningful improvement in pain or general disability with the SPADI. The patient did demonstrate a meaningful improvement in sport-specific function with the DASH. It is possible that sport-specific plyometric rehabilitation may have provided additional benefit for this athlete's ability to return to sport, but definite conclusions regarding treatment effectiveness are limited by the case report design. Properly designed studies investigating the benefits of sport-specific plyometric rehabilitation are warranted before the effectiveness of these techniques can be determined.