The aim of the study is to investigate the efficacy of targeted scapular stabilization exercise in shoulder pain. This is an evaluator-blinded, multicenter, randomized controlled trial. The scapular stabilization exercise group ( n = 45) received scapular stabilization exercise based on the type of scapular dyskinesis for 6 wks; the conventional exercise group ( n = 45) received pendulum, wall climbing and stick exercises for 6 wks. Constant-Murley score, numerical rating scale, range of motion, type of scapular dyskinesis, lateral scapular sliding test, pectoralis minor index, scapular index, and satisfaction were assessed at baseline, 2-, 4-, and 6-wk treatment as well as a 6-wk follow-up. After a 6-wk intervention, the improvement of Constant-Murley score was greater in the scapular stabilization exercise group than in the conventional exercise group, and improvement continued at the 6-wk follow-up ( F = 15.39, P < 0.001, partial η 2 = 0.17). The results were also significant for numerical rating scale during activity, lateral scapular sliding test, pectoralis minor index, type of scapular dyskinesis, and satisfaction in favor of the scapular stabilization exercise group ( P < 0.05). Targeted scapular stabilization exercise is an effective intervention program that might be applied to the rehabilitation of shoulder pain.