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Background: Scapular dyskinesis is defined as abnormal movement during dynamic activities of the shoulder. Individuals with various shoulder pathologies may demonstrate altered kinematics and muscle activation. However, clinical assessment of scapular dyskinesis is inconsistently related to present or future symptoms, and patients may experience improvements in symptoms and function without concomitant changes in scapular mechanics. Thus, the purpose of this case report is to highlight limitations in the diagnostic and prognostic value of scapular dyskinesis and describe improvements in an individual’s shoulder pain and function following training of the shoulder complex despite continued dyskinesis. Case Description: This case follows a patient who presented to the clinic for shoulder, neck, and periscapular pain of 10 weeks duration. He had noticeable scapular dyskinesis during physical examination that reproduced his pain. Intervention: Load management and activity modifications were discussed during the initial stages to decrease symptom irritability. A motor control focused approach was used to restore pain-free range of motion and change scapular kinematics. Mid and late-stage rehabilitation aimed to restore global tissue capacity and expand his envelope of function through strength training and plyometric activities. Outcome Measures: Pain, subjective questionnaires, the Scapular Dyskinesis Test, and tolerance to work and recreation were used to measure improvement. Discussion: The diagnosis of scapular dyskinesis in an individual with shoulder pain may be secondary to their symptoms or represent normal movement variability. The patient in this case report demonstrated improved function and decreased pain despite lingering asymmetries in scapular kinematics. Therefore, a rehabilitation approach aimed at restoring tissue capacity and improving function may be successful independent of kinematic changes.