BackgroundFatigue is one of the most prevalent and burdensome symptoms for patients with inflammatory bowel disease (IBD). Although fatigue increases during periods of inflammation, for some patients it persists when disease is in remission. Compared to other long-term conditions where fatigue has been extensively researched, optimal management of fatigue in patients with IBD is unknown and fatigue has rarely been the primary outcome in intervention studies. To date, interventions for the management of IBD-fatigue are sparse, have short-term effects and have not been implemented within the existing health system. There is a need to integrate current best evidence across different conditions, patient experience and clinical expertise in order to develop interventions for IBD-fatigue management that are feasible and effective. Modifying an existing intervention for patients with multiple sclerosis, this study aims to assess the feasibility and initial estimates of efficacy of a cognitive behavioural therapy (CBT) intervention for the management of fatigue in patients with IBD.MethodsThe study will be a two-arm pilot randomised controlled trial. Patients will be recruited from one outpatient IBD clinic and randomised individually to either: Group 1 (CBT manual for the management of fatigue, one 60-min session and seven 30-min telephone/Skype sessions with a therapist over an eight-week period); or Group 2 (fatigue information sheet to use without therapist help). Self-reported IBD-fatigue (Inflammatory Bowel Disease-Fatigue Scale) and IBD-quality of life (United Kingdom Inflammatory Bowel Disease Questionnaire) and self-reported disease activity will be collected at baseline, three, six and 12 months post randomisation. Illness perceptions, daytime sleepiness, anxiety and depression explanatory variables will be collected only at three months post randomisation. Clinical and sociodemographic data will be retrieved from the patients’ medical notes. A nested qualitative study will evaluate patient and therapist experience, and healthcare professionals’ perceptions of the intervention.DiscussionThe study will provide evidence of the feasibility and initial estimates of efficacy of a CBT intervention for the management of fatigue in patients with IBD. Quantitative and qualitative findings from the study will contribute to the development and implementation of a large-scale randomised controlled trial assessing the efficacy of CBT interventions for IBD-fatigue.Trial registrationISRCTN Registry, ISRCTN17917944. Registered on 2 September 2016.Electronic supplementary materialThe online version of this article (doi:10.1186/s13063-017-1926-3) contains supplementary material, which is available to authorized users.