Crohn's disease (CD) is a long-term inflammatory gastrointestinal disorder, often adversely affecting physical, emotional, and psychological well-being. Pharmaceutical management is habitually adopted; although medicinal therapies require continuous administration, and are often associated with significant side effects and low adherence rates. Whole body vibration (WBV) represents a non-invasive technique, that provides vibration stimulation to the entire body. As WBV appears to target the physiological pathways and symptoms pertinent to CD epidemiology, it may have significant potential as a novel non-pharmaceutical intervention therapy in CD. This paper presents the study protocol for a randomised controlled trial investigating the impact of WBV on health outcomes in individuals with CD. This 6-week, parallel randomised controlled trial will recruit 168 individuals, assigned to receive WBV and lifestyle education 3 times per week compared to control, receiving lifestyle education only. The primary outcome of the trial will be the difference from baseline to post-intervention in health-related quality of life between the groups, assessed with the Inflammatory Bowel Disease Quality of Life Questionnaire. Secondary outcomes will include between-group differences in other questionnaires assessing fatigue, anxiety and pain, measures of physical fitness, and biological markers for disease activity and inflammation. Statistical analyses will follow an intention-to-treat approach, using linear mixed-effects models to compare changes between time points and both trial groups. Ethical approval was granted by the Nottingham Research Ethics Committee (REC: 24/EM/0106) and the study has been registered prospectively as a clinical trial (NTC06211400).