Introduction Exercise interventions have been widely investigated in patients with cancer and demonstrate beneficial effects. However, intervention studies that include older women with breast cancer exercising during medical treatment are scarce. Hence, the aim of this study is to investigate the effect of a 12-week exercise-based intervention in older women (≥65 years) with breast cancer receiving (neo)adjuvant or first-line or second-line systemic therapy. Methods and analysis This is a single-centre, two-armed randomised controlled trial. We anticipate including 100 patients, who will be randomised 1:1 to exercise-based intervention or control stratified by treatment setting ((neo)adjuvant or metastatic) and treatment (chemotherapy or endocrine therapy + cyclin-dependent kinase (CDK) 4/6 inhibitors). The intervention group will receive standard oncological treatment and a 12-week supervised exercise-based intervention comprising a progressive resistance exercise programme two times per week, a protein supplement after exercise and a home-based walking programme based on daily step counts. The control group will receive standard oncological treatment. Assessments will be performed at baseline and 6, 12 and 24 weeks after start of the intervention. Primary outcome is physical function, measured by the 30-second Chair Stand Test. Secondary outcomes are feasibility (compliance and adherence to intervention), objective and patient-reported functional measures (6-meter and 10-meter gait speed; 6-min Walk Test; Handgrip Strength; Stair Climb Test; Physical Activity Questionnaire), symptom burden and well-being (MD Anderson Symptom Inventory; Hospital Anxiety and Depression Scale), quality of life (European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core-30 and B23), body composition (dual-energy X-ray absorptiometry scan), side effects, inflammatory biomarkers, hospitalisation and survival. Ethics and dissemination The protocol was reviewed and accepted by the Scientific Ethics Review Committee of the Capital Region of Denmark, 17 June 2018 (VEK ref.: H-18021013). Trial results will be submitted for publication in a peer-reviewed journal and presented on conferences, in oncology wards, exercise centres in municipalities and patient organisations, ensuring dissemination to relevant stakeholders. Trial registration number https://clinicaltrials.gov/on 3 September 2018. Identifier: NCT03656731.