The purpose of this clinical trial is to compare the effectiveness of a scapular-focused treatment with a control therapy in patients with shoulder impingement syndrome. Therefore, a randomized clinical trial with a blinded assessor was used in 22 patients with shoulder impingement syndrome. The primary outcome measures included self-reported shoulder disability and pain. Next, patients were evaluated regarding scapular positioning and shoulder muscle strength. The scapular-focused treatment included stretching and scapular motor control training. The control therapy included stretching, muscle friction, and eccentric rotator cuff training. Main outcome measures were the shoulder disability questionnaire, diagnostic tests for shoulder impingement syndrome, clinical tests for scapular positioning, shoulder pain (visual analog scale; VAS), and muscle strength. A large clinically important treatment effect in favor of scapular motor control training was found in self-reported disability (Cohen's d = 0.93, p = 0.025), and a moderate to large clinically important improvement in pain during the Neer test, Hawkins test, and empty can test (Cohen's d 0.76, 1.04, and 0.92, respectively). In addition, the experimental group demonstrated a moderate (Cohen's d = 0.67) improvement in self-experienced pain at rest (VAS), whereas the control group did not change. The effects were maintained at three months follow-up.