PurposeProximal hamstring tendinopathy (PHT) presents as localised lower buttock pain with tasks such as squatting and sitting. It is a condition that occurs at all ages and levels of sporting participation and can cause disability with sport, work, and activities of daily living.This paper details a pilot trial protocol for investigating the effectiveness of individualised physiotherapy compared to extracorporeal shockwave therapy (ESWT) on pain and strength in people with PHT.MethodsThe study is an assessor-blinded, pilot randomised controlled trial (RCT). One hundred participants with PHT will be recruited from the local community and sporting clubs. Participants will be randomised to receive six sessions of either individualised physiotherapy or ESWT, with both groups also receiving standardised education and advice.Primary outcomes will be global rating of change on a 7-point Likert scale, and the Victorian Institute of Sport—Hamstring (VISA-H) scale, measured at 0, 4, 12, 26 and 52 weeks. Secondary outcomes will include sitting tolerance, the modified Physical Activity Level Scale, eccentric hamstring strength, modified Tampa scale for kinesiophobia, the Örebro Musculoskeletal Pain Screening Questionnaire Short Form (ÖMPSQ-SF), Numerical Pain Rating Scale (NPRS) for average and worst pain, participant adherence, the Pain Catastrophizing scale, satisfaction scores, and quality of life. Data will be analysed on an intention to treat basis, with between-group effects estimated using linear mixed models for continuous data and Mann Whitney U tests for ordinal data.ConclusionsThis pilot RCT will compare individualised physiotherapy versus ESWT for PHT. The trial will determine feasibility and estimated treatment effects to inform a definitive trial in the future.Trial registrationThe trial has been prospectively registered with the Australia & New Zealand Clinical Trials Registry (ACTRN12621000846820), registered 1 July 2021,https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=373085Supplementary InformationThe online version contains supplementary material available at 10.1186/s40634-023-00615-x.