This study tested the effect of individualised advice to increase physical activity and/or omega-3 fatty acid suppleme ntation on fatigue in inactive inflammatory bowel disease (IBD). Patients in remission were recruited to a pilot study using a randomised controlled 2x2 factorial design comparing baseline and post-intervention fatigue scores. Interventions (12 weeks) were 15-minute exercise consultation and/or 2970 mg/day omega-3 supplementation and controls were general health discussion and/or placebo. From n=656 screened patients, n=74 who met the eligibility criteria were random ised, n=60 commenced and n=52 completed the study. Fatigue measured with Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-F) score was worse with omega-3 supplementation and unchanged with exercise advice. Fatigue, measured by Inflammatory Bowel Disease-Fatigue (IBD-F) score, was reduced with exercise advice. Advice to increase physical activity and omega-3 supplementation, singly or in combination, was shown to be well-tolerated in IBD patients in remission. There was no evidence of exercise-related adverse effects on gut symptoms. Fatigue (IBD-F score) was reduced with exercise advice, but fatigue (FACIT-F score) was unchanged. Increasing fatigue with omega-3 supplementation is unexplained. Regular exercise may be a self-management option in IBD-related fatigue.