Introduction People presenting with shoulder pain considered to be of musculoskeletal origin is common in primary care but diagnosing the cause of the pain is contentious, leading to uncertainty in management. To inform optimal primary care for patients with shoulder pain, the study aims to (1) to investigate the short-term and long-term outcomes (overall prognosis) of shoulder pain, (2) estimate costs of care, (3) develop a prognostic model for predicting individuals' level and risk of pain and disability at 6 months and (4) investigate experiences and opinions of patients and healthcare professionals regarding diagnosis, prognosis and management of shoulder pain. Methods and analysis The Prognostic And Diagnostic Assessment of the Shoulder (PANDA-S) study is a longitudinal clinical cohort with linked qualitative study. At least 400 people presenting to general practice and physiotherapy services in the UK will be recruited. Participants will complete questionnaires at baseline, 3, 6, 12, 24 and 36 months. Short-term data will be collected weekly between baseline and 12 weeks via Short Message Serevice (SMS) text or software application. Participants will be offered clinical (physiotherapist) and ultrasound (sonographer) assessments at baseline. Qualitative interviews with ≈15 dyads of patients and their healthcare professional (general practitioner or physiotherapist). Short-term and long-term trajectories of Shoulder Pain and Disability Index (using SPADI) will be described, using latent class growth analysis. Health economic analysis will estimate direct costs of care and indirect costs related to work absence and productivity losses. Multivariable regression analysis will be used to develop a prognostic model predicting future levels of pain and disability at 6 months using penalisation methods to adjust for overfitting. The added predictive value of prespecified physical examination tests and ultrasound findings will be examined. For the qualitative interviews an inductive, exploratory framework will be adopted using thematic analysis to investigate decision making, perspectives of patients and clinicians on the importance of diagnostic and prognostic information when negotiating treatment and referral options. Ethics and dissemination The PANDA-S study has ethical approval from Yorkshire and The Humber-Sheffield Research Ethics Committee, UK (18/YH/0346, IRAS Number: 242750). Results will be disseminated through peer-reviewed publications, social and mainstream media, professional conferences, and the patient and public involvement and engagement group supporting this study, and through newsletters, leaflets and posters in participating sites.