BACKGROUND: Persons with multiple sclerosis (PwMS) often have reduced aerobic capacity and report fatigue as the most disabling symptom impacting their health-related quality of life (HRQoL). A multidisciplinary rehabilitation approach is recommended for successful management of symptoms, although there is little supporting evidence. The aim of this study is to evaluate the effect of a multimodal therapy approach, including endurance training and patient education, during a three-week inpatient rehabilitation stay, on HRQoL in PwMS at six months follow-up. Inpatient energy management education (IEME) + high-intensity interval training (HIIT) will be compared with progressive muscle relaxation (PMR) + moderate continuous training (MCT). METHODS: This study has a two-armed single-blind randomized controlled superiority trial design. One hundred six PwMS-related fatigue (relapsing-remitting or chronic progressive phenotypes; Expanded Disability Status Scale (EDSS) ≤ 6.5) will be recruited at the Valens clinic, Switzerland, and randomized into either an experimental (EG) or a control group (CG). EG: participants will perform IEME twice and HIIT three times per week during the three-week rehabilitation stay. IEME is a group-based intervention, lasting for 6.5 h over three weeks. HIIT contains of five 1.5-min high-intensive exercise bouts on a cycle ergometer at 95-100% of peak heart rate (HR), followed by active breaks of unloaded pedalling for 2 min to achieve 60% of HR. CG: participants will perform PMR twice and MCT three times per week during the three-week rehabilitation stay, representing local usual care. PMR consists of six 1-h relaxation group sessions. MCT consists of 24-min continuous cycling at 65% of HR. The primary outcome is HRQoL (Physical and Mental Component Summaries of the Medical Outcome Study 36-item Short Form Health Survey; SF-36), measured at entry to the clinic (baseline, T), three weeks after T (T) and at four (T) and six (T) months after T. Secondary outcomes comprise cardiorespiratory fitness, inflammatory markers (measured at T and T), fatigue, mood, self-efficacy, occupational performance, physical activity (measured at T, T, T and T) and behaviour changes in energy management (measured at T and T). DISCUSSION: This study will provide detailed information on a multimodal therapy approach to further improve rehabilitation for PwMS. TRIAL REGISTRATION: This trial was prospectively registered at ClinicalTrials.gov ( NCT04356248 ; 22 April 2020).