Background: There are limited treatment options for mental health comorbidities associated with Inflammatory Bowel Disease (IBD), although they have been shown to negatively affect the course of IBD and multiple important areas of functioning. Photobiomodulation (PBM) is a new therapeutic intervention using laser-generated low-powered light therapy that has shown early promise in alleviating fatigue, depression, and pain in chronic illness. Methods: This prospective, single-arm pilot study aims to assess the feasibility and efficacy of PBM in the treatment of fatigue, depression, and pain in youth with IBD. We will recruit 28 young adults with IBD who will receive PBM in addition to treatment as usual. The primary outcome will be fatigue, while secondary outcomes will include depression, pain, quality of life, inflammatory markers, alterations in microbiome composition, physical activity, and functioning. Outcome measures will be assessed at baseline, after a 10-week control period (pre-PBM), at 20 weeks (post-PBM), and at 30 weeks. Feasibility will be assessed by attendance, recruitment rates, and participants’ views of PBM. Mixed-effects linear regression modelling will be used to assess the PBM effect on continuous outcomes (fatigue, depression, anxiety and stress scores, and inflammation levels). Results: The study will provide preliminary indicators of PBM feasibility and efficacy in IBD.