The aim of this study was to evaluate if manual therapy added to a therapeutic exercise program produced greater improvements than a sham manual therapy added to same exercise program in patients with non-specific shoulder pain. This was an evaluator-blinded randomized controlled trial. Forty-five subjects were randomly allocated into one of three groups: manual therapy (glenohumeral mobilization technique and rib-cage technique); thoracic sham manual therapy (glenohumeral mobilization technique and rib-cage sham technique); or sham manual therapy (sham glenohumeral mobilization technique and rib-cage sham technique). All groups also received a therapeutic exercise program. Pain intensity, disability and pain-free active shoulder range of motion were measured post treatment and at 4-week and 12-week follow-ups. Mixed-model analyses of variance and post hoc pairwise comparisons with Bonferroni corrections were constructed for the analysis of the outcome measures. All groups reported improved pain intensity, disability and pain-free active shoulder range of motion. However, there were no between-group differences in these outcome measures. The addition of the manual therapy techniques applied in the present study to a therapeutic exercise protocol did not seem to add benefits to the management of subjects with non-specific shoulder pain.