IntroductionRotator cuff calcific tendinopathy (RCCT) involves calcific deposits in the rotator cuff. Non-surgical interventions such as extracorporeal shockwave therapy (ESWT) and ultrasound-guided percutaneous irrigation of calcific tendinopathy (US-PICT) are recommended for its early management. Exercise therapy (ET) has shown to be an effective intervention for people with rotator cuff tendinopathy, but it has not been formally tested in RCCT. The main objective of this study is to compare the effectiveness of an ET programme with ESWT and US-PICT in people with RCCT. As a secondary aim, this study aims to describe the natural history of RCCT.Methods and analysisA randomised, single-blinded four-group clinical trial will be conducted. Adults from 30 to 75 years diagnosed with RCCT who accomplish eligibility criteria will be recruited. Participants (n=116) will be randomised into four groups: ET group will receive a 12-week rehabilitation programme; ESWT group will receive four sessions with 1 week rest between sessions during 1 month; US-PICT group will receive two sessions with 3 months of rest between sessions; and (actual) wait-and-see group will not receive any intervention during the 12-month follow-up. The primary outcome will be shoulder pain assessed with the Shoulder Pain and Disability Index at baseline, 2 weeks, 4 months, 6 months and 12 months from baseline. The primary analysis will be performed at 12 months from baseline. Secondary outcomes will include pain, range of motion, patient satisfaction and imaging-related variables. Moreover, the following psychosocial questionnaires with their corresponding outcome measure will be assessed: Central Sensitization Inventory (symptoms related to central sensitization); Pain Catastrophizing Scale (pain catastrophizing); Tampa Scale for Kinesiophobia 11 items (fear of movement); Fear Avoidance Belief Questionnaire (fear avoidance behaviour); Hospital Anxiety and Depression Scale (anxiety and depression); Pittsburgh Sleep Quality Index (sleep quality); and the EuroQol-5D (quality of life). An intention-to-treat analysis will be performed to reduce the risk of bias using a worst-case and best-case scenario analysis.Ethics and disseminationEthics committee approval for this study has been obtained (reference number: 1718862). The results of the main trial will be submitted for publication in a peer-reviewed journal.Trial registration numberNCT05478902.