A disturbance in scapulohumeral rhythm may cause negative biomechanic effects on rotator cuff (RC). Alteration in scapular motion and shoulder pain can influence RC strength. Purpose of this study was to assess supraspinatus and infraspinatus strength in 29 overhead athletes with scapular dyskinesis, before and after 3 and 6 months of rehabilitation aimed to restore scapular musculature balance. A passive posterior soft tissues stretching was prescribed to balance shoulder mobility. Scapular dyskinesis patterns were evaluated according to Kibler et al. Clinical assessment was performed with the empty can (EC) test and infraspinatus strength test (IST). Strength values were recorded by a dynamometer; scores for pain were assessed with VAS scale. Changes of shoulder IR were measured. The force values increased at 3 months (P < 0.01) and at 6 months (P < 0.01). Changes of glenohumeral IR and decrease in pain scores were found at both follow-up. Outcomes registered on pain and strength confirm the role of a proper scapular position for an optimal length-tension relationship of the RC muscles. These data should encourage those caring for athletes to consider restoring of scapular musculature balance as essential part of the athletic training.