Shoulder tendon injuries are common clinical conditions and are a significant source of pain and dysfunction. These conditions are more common in individuals who perform repetitive overhead activities and in individuals who have abnormal scapular kinematics, termed scapular dyskinesis (SD). However, the long term consequences associated with overuse activity in the presence of SD are unknown. Therefore, the objective of this study was to determine the effect of overuse in combination with SD on joint mechanics and properties of the rotator cuff and biceps tendons. A rat model of scapular dyskinesis was used. Ninety adult male Sprague-Dawley rats (400-450 g) were randomized into three groups: nerve transection (SD), sham nerve transection + overuse (OV), or nerve transection + overuse (SD + OV). Rats were sacrificed at 2, 4, and 8 weeks after surgery. Shoulder function and passive joint mechanics were evaluated over time and tendon properties (mechanical, histological, organizational, and compositional) were measured. Results demonstrated that overuse activity and SD are each independently detrimental to tendon properties (e.g., diminished mechanical properties, disorganized collagen). However, tendon damage caused by the addition of overuse may be worse, with more parameters altered, than damage caused by the addition of SD. This study helps define the mechanical mechanisms leading to tendon damage and provides a framework for distinguishing treatment strategies for active patients and those with abnormal scapular mechanics.