36 patients diagnosed with rotator cuff tendinopathy were included in this trial to compare the efficacy of 12-week eccentric and conventional exercise programs. Outcomes were evaluated over a 26-week follow-up period and included shoulder function evaluated using the Constant-Murley score, pain, range of motion, and shoulder strength. Both groups demonstrated significant improvements in shoulder function and pain from baseline over the 26-week follow-up. There were no significant differences between the two exercise programs over the 26-week follow-up, indicating that eccentric exercises are an effective form of exercise therapy for rotator cuff tendinopathy. Larger randomized controlled trials are needed to corroborate the findings of this trial.