Background Recently, Recently, the use of spinal manual therapy to treat shoulder pain has garnered attention. Clinical evidence has shown that spinal manual therapy is a common therapeutic approach used to address extremity dysfunction like Shoulder Impingement Syndrome (SIS). Purpose To investigate whether thoracic manipulation is more beneficial than treatment directed solely at the shoulder for patients with SIS on scapular kinematics and scapular muscle strength ratio. Methods With ethical approval and informed consent, 55 participants aged between 20 and 45 participated in this study as SIS (stage I and II Neer’s classification) and were recruited to a randomized controlled study. The selected subjects were randomly assigned into experimental and control groups. The experimental group received conventional physical therapy treatment based on the most evidence-based treatment for SIS (Stretching of the posterior capsule, rotator cuff strengthening, and scapular muscle training), and real thoracic spine manipulation. The control group received the same interventions. However, they were treated with sham thoracic manipulation. Scapular upward rotation was measured in 2 positions: 90° and 180° of elevation in the scapular plane by baseline bubble inclinometer, scapular tipping was measured by acromion to table distance (A-T distance), and the isometric strength of both Upper Trapezius (UT), Serratus Anterior (SA) and lower trapezius (LT) were assessed using Hand Held Dynamometer (HHD) device and then the UT/SA ratio and UT/LT ratios were calculated. All outcome measures were assessed at baseline, after 1 session, and after 6 and 12 weeks. Results Both groups showed significant improvements in terms of scapular upward rotation, scapular tipping, and scapular isometric muscle strength after 6 and 12 weeks (P<0.05, Cohen’s d = 0.6), but the control group showed no significant improvement after one session in terms of scapular upward rotation and scapular tipping (P > 0.05, Cohen’s d = 0.4). Between-group results showed a significant difference favoring the experimental group in scapular upward rotation, scapular tipping, UT/SA ratio, and UT/LT ratios (P<0.05, Cohen’s d=0.72, Cohen’s d=0.68, Cohen’s d=0.63, Cohen’s d=0.53, respectively). Conclusion(s) The addition of manual therapy directed to the thoracic spine along with exercise therapy showed clinically and statistically significant results for scapular kinematics and scapular muscle strength ratio. It demonstrated superior effects than exercise therapy alone for the treatment of patients with SIS. Implications The significant improvement in the UT/SA and UT/LT muscle strength ratios indicates that thoracic manipulation may help address muscle imbalances that contribute to abnormal scapular motion in SIS. Clinicians should assess scapular muscle imbalances and consider spinal manipulation as part of a comprehensive approach to correcting these issues.