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Introduction Regular physical activity and limiting sedentary behaviour are important aspects in managing multiple sclerosis (MS). Fatigue is a common and disabling symptom in MS, contributing to impairments in activities of daily living and poorer quality of life. This study aims to determine the effectiveness of a physical activity and sedentary behaviour intervention, called iStep-MS, for reducing fatigue in people with MS when delivered across the MS care pathway.Methods and analysis This is a multicentre, two-arm randomised controlled superiority trial with embedded economic and process evaluations. The study will take place across South-East England in acute and community National Health Service settings and charity-funded MS and neurological therapy centres. Intervention deliverers will include a range of healthcare staff such as physiotherapists, occupational therapists, therapy assistants, nurses and exercise therapists. A target sample size of n=198 participants will be randomised 1:1 to the intervention (iStep-MS behaviour change intervention plus usual care) or control (usual care only) arms. Participants will be adults with any type of MS, experiencing MS-related fatigue, relapse-free for >3 months, with a Self-Reported Disability Status Scale category of ≤3.5 (no disability to moderate disability) or 4–6.5 (significant disability). The iStep-MS intervention includes four one-to-one consultation sessions in-person or online with an intervention deliverer over 3 months, incorporating behaviour change techniques aimed at increasing physical activity and reducing sedentary behaviour. The consultations are supported by a handbook designed to help individuals with MS set goals and achieve behavioural changes and a wearable activity tracker for self-monitoring. Outcomes (assessed at baseline, 3 months and 9 months) include self-reported fatigue, quality of life, MS-impact, walking capability, pain, self-efficacy and waist circumference. Sitting, standing and stepping will be measured over 8 days using the activPAL4 device. A process evaluation will assess intervention acceptability, adherence and fidelity, including questionnaires and focus groups with participants and deliverers. A cost-effectiveness analysis will evaluate the value for money of the intervention against usual care.Ethics and dissemination Ethical approval has been granted by the NHS London—Bloomsbury Research Ethics Committee (reference 25/LO/0272). Results will be disseminated in scientific journals, conferences and to the wider public (eg, newsletters and social media).Trial registration number ISRCTN16944301.