INTRODUCTION: Inflammatory bowel disease (IBD) is a chronic autoinflammatory disease of the gastrointestinal tract with peak age of onset during adolescence and young adulthood. Adolescents and young adults (AYAs) with IBD experience higher depression rates compared with peers who are well or have other chronic conditions. Mindfulness-based interventions are of particular interest because of their potential to improve both the course of IBD and depression. METHODS AND ANALYSIS: This study is a parallel design, single-blind, pilot randomised controlled trial (RCT) of mindfulness-based cognitive therapy (MBCT) in AYAs with IBD and depression. The trial aims to recruit 64 participants who will be randomly allocated to MBCT or treatment as usual. The primary outcome measure is the depression subscale score from the Depression, Anxiety and Stress Scale. Secondary outcomes include anxiety, stress, post-traumatic growth, IBD-related quality of life, illness knowledge, medication adherence, mindfulness, IBD activity, inflammatory markers, microbiome and brain neuroconnectivity changes. All outcomes other than neuroimaging will be collected at three time points: at baseline, at therapy completion and at 20 weeks. Neuroimaging will be conducted at baseline and at therapy completion. Mixed-effects linear and logistic regression modelling will be used to analyse continuous and dichotomous outcomes, respectively. Participants' experiences will be explored through focus groups, and thematic analysis will be used to generate relevant themes. ETHICS AND DISSEMINATION: The protocol has been approved by the Mater Hospital Human Research Ethics Committee (HREC) and University of Queensland HREC. Trial findings will be published in peer-reviewed journals and will be presented at scientific conferences. TRIAL REGISTRATION NUMBER: ACTRN12617000876392, U1111-1197-7370; Pre-results.