Background: Structured exercise training has been proposed as a useful adjunctive therapy for Crohn’s disease by improving immune function and psychological health, reducing fatigue, and promoting gains in muscle and bone strength. However, the evidence for exercise in Crohn’s disease is sparse, with only a handful of small prospective trials, with methodological limitations, including the use of non-randomised and non-controlled study designs and small sample sizes. Here, we describe the protocol for a study that aims to assess the feasibility and acceptability of two common types of exercise training – high-intensity interval training (HIIT) and moderate-intensity continuous training (MICT) – in adults with inactive or mildly active CD. Methods: This is a randomised, controlled, assessor-blinded, feasibility trial with three parallel groups. Forty-five adults with inactive or mildly-active Crohn’s disease will be randomly assigned 1:1:1 to HIIT, MICT, or usual care control. Participants in the HIIT and MICT groups will be invited to undertake three sessions of supervised exercise each week for 12 consecutive weeks. HIIT sessions will consist of ten 1-minute intervals of cycling exercise at 90% of peak power output separated by 1 minute of active recovery. MICT sessions will involve 30 minutes of continuous cycling at 35% of peak power output. Participants will be assessed before randomisation and 13 and 26 weeks after randomisation. Feasibility outcomes include rates of recruitment, retention and adherence. Interviews with participants will explore the acceptability of the exercise programmes and study procedures. Clinical/health outcomes include cardiorespiratory fitness, body mass index, resting blood pressure, markers of disease activity (faecal calprotectin and Crohn’s Disease Activity Index), and activated T-cell cytokine profiles. Study questionnaires include the Inflammatory Bowel Disease Quality of Life Questionnaire, EQ-5D-5L, IBD Fatigue Scale, Hospital and Anxiety Depression Scale, and International Physical Activity Questionnaire. Discussion: This study will provide useful information on the feasibility and acceptability of supervised exercise training in adults with inactive and mildly-active Crohn’s disease, and will inform the design of a subsequent, adequately-powered, multi-centre trial.