Wheelchair basketball is one of the most popular Paralympic sports, including players with different diagnoses. To date, there is scarce evidence on shoulder functionality in wheelchair basketball players, and there is no consensus on a shoulder injury prevention program in these athletes. Therefore, in the present pilot study, we aimed to evaluate the effects of a comprehensive rehabilitative approach on shoulder ROM, muscle activity, and functioning in wheelchair basketball athletes. We included adult wheelchair basketball athletes playing in the Italian Second League who completed an 8-week comprehensive rehabilitative program, based on education to avoid upper limb pain injuries, preventive exercises, and improvement of ergonomics through kinematic analysis. We administered the Wheelchair User’s Shoulder Pain Index (WUSPI) and the Kerlan-Jobe Orthopaedic Clinic (KJOC) questionnaire to evaluate pain experienced during functional activities, and used kinematic analysis integrated with sEMG to evaluate shoulder function and propulsion pattern. A sample of 10 wheelchair athletes (33.75 ± 6.42 years) were assessed. After the intervention there was a significant (p < 0.05) difference in WUSPI score (27.0 ± 18.5 vs. 25.0 ± 21.5) and in KJOC score (89.3 ± 10.4 to 95.4 ± 9.1). Moreover, there was a significant improvement in scapular upward rotation, abduction, and extra-rotation of the glenohumeral joint. Propulsion techniques improved in pattern and acceleration. This approach played a key role in improving upper limb function, reducing the incidence of pain and cumulative trauma disorders. However, the small sample size could affect the generalizability of results. In conclusion, healthcare professionals should monitor wheelchair athletes, assessing the patient’s function, ergonomics, equipment, and level of pain, and introducing specific exercises to prevent upper limb injuries.