Background: Shoulder pain is common, with a lifetime prevalence of up to 67%. Evidence is conflicting in relation to imaging findings and pain in the shoulder. Sonoelastography can be used to estimate tissue stiffness and may be a clinically relevant technique for diagnosing and monitoring tendon healing. Purpose: To evaluate changes in supraspinatus tendon stiffness using strain elastography (SEL) and associations with changes in patient-reported outcomes, supraspinatus tendon thickness, and grade of tendinopathy after 12 weeks of unilateral shoulder exercises in patients with supraspinatus tendinopathy. Study Design: Controlled laboratory study. Methods: A total of 23 patients with unilateral clinical supraspinatus tendinopathy performed 12 weeks of “standard care” exercises. At baseline and follow-up, supraspinatus tendon stiffness was measured bilaterally using SEL and compared with tendinopathy grading on magnetic resonance imaging scans and tendon thickness measured using conventional ultrasound. Patient-reported outcome measures included physical function and symptoms from the Disabilities of the Arm, Shoulder and Hand questionnaire and pain rating (visual analog scale). Results: No significant changes in SEL within or between groups (asymptomatic vs symptomatic tendon) were seen. All patient-reported outcomes showed significant improvement from baseline to follow-up, but with no change in tendinopathy grading and tendon thickness. No significant differences in the proportion of patients changing above the minimal detectable change in SEL and PROM were seen, except for discomfort while sleeping. Conclusion: Despite no significant within-group or between-group changes in SEL, significant improvements were found in patient-reported outcomes. An acceptable agreement between patients changing above the minimal detectable change in SEL and patient-reported outcome measure was seen. Further studies should explore the use of SEL to detect changes after tendon repair and long-term training potentially in subgroups of different tendinopathy phases. Clinical Relevance: In the short term, structural changes in supraspinatus tendons could not be visualized using SEL, indicating that a longer time span should be expected in order to observe structural changes, which should be considered before return to sports. Subgrouping based on stage of tendinopathy may also be important in order to evaluate changes over time with SEL among patients with supraspinatus tendinopathy. Registration: NCT03425357 (ClinicalTrials.gov identifier).