Introduction: Shoulder pain is a condition of high prevalence in the general population. Studies indicate that physiotherapeutic treatment with exercise is effective in reducing pain and restoring function in patients with shoulder pain. Patients may have difficulty accessing the physiotherapy service due to the cost of treatment, transportation to the service, and long waiting lines. A possible solution is the use of a web-based exercise prescription instrument to increase access to physiotherapy for shoulder pain patients. Objective: To verify the effects of an intervention with a web-based instrument compared to a in person and supervised intervention. Methods: This study is a controlled, randomized, blinded clinical trial. There will be 184 individuals with shoulder pain who will be randomly assigned to two groups. One group will receive a web-based instrument intervention and the other group will receive the in person and supervised intervention. The intervention will consist of strengthening exercises with emphasis on the lateral rotator and scapulothoracic muscles. The primary outcome will be pain and disability (SPADI, Shoulder Pain and Disability Index), and the secondary outcomes will be function (DASH questionnaire, Disabilities of the Arm, Shoulder and Hand), self-efficacy (CPSS, Chronic Pain Self-Efficacy Scale), kinesiophobia (Cover Scale), patient expectation of treatment (7-point Likert Scale), and patient satisfaction (Global Change Assessment Scale). All outcomes will be measured before and after 12 weeks of treatment (2x/week), after 6 months and 12 months from the end of treatment. Normality of data will be verified by Kolmogorov Smirnov's test. Differences between groups will be verified using the mixed linear models with the interaction terms versus time. The effect size will be calculated for the variables between the groups. The significance level will be set at 5%.

Inclusion Criteria:

• Age 18-60;
• Self-reported pain of intensity equal to or greater than 3 points on the numerical pain scale (NDT) at rest or arm movement in the anterolateral region of the shoulder;
• Duration of at least 3 months of shoulder pain;
• Have a mobile phone with Android 4.1 or higher.

Exclusion Criteria:

• History of trauma related to the onset of symptoms;
• History of clavicle, scapula or humerus fracture;
• History of surgical stabilization or rotator cuff repair;
• History of shoulder dislocation;
• Pain related to the cervical spine;
• Adhesive capsulitis;
• Systemic disease involving the joints and cognitive alteration that makes it impossible to carry out questionnaires or use the mobile application.

At the end of the clinical trial will be published the Study Protocol and Statistical Analysis Plan (SAP), if any researcher wants more information can request. The Informed Consent Form (ICF) can also be available.