Background: Studies have demonstrated usefulness of cognitive-behavioural therapy (CBT) in managing distress in inflammatory bowel disease (IBD); however, few have focused on IBD course. The present trial aimed to investigate whether adding CBT to standard treatment prolongs remission in IBD in comparison to standard therapy alone. Methods: A 2-arm parallel pragmatic randomised controlled trial (+CBT - standard care plus either face-to-face (F2F) or online CBT over 10 weeks versus standard care alone (SC)) was conducted with adult patients in remission. IBD remission at 12 months since baseline was the primary outcome measure while the secondary outcome measures were mental health status and quality of life (QoL). Linear mixed-effect models were used to compare groups on outcome variables while controlling for baseline. Results: Participants were 174 patients with IBD (90 +CBT, 84 SC). There was no difference in remission rates between groups, with similar numbers flaring at 12 months. Groups did not differ in anxiety, depression or coping at 6 or 12 months (p >0.05). When only participants classified as 'in need' (young, high baseline IBD activity, recently diagnosed; poor mental health) were examined in the post-hoc analysis (n = 74, 34 CBT and 40 controls), CBT significantly improved mental QoL (p = .034, d = .56) at 6 months. Online CBT group had a higher score on Precontemplation than the F2F group, which is consistent with less developed coping with IBD in the cCBT group (p = .045). Conclusions: Future studies should direct psychological interventions to patients 'in need' and attempt to recruit larger samples to compensate for significant attrition when using online CBT. Trial registration: The protocol was registered on 21/10/2009 with the Australian New Zealand Clinical Trials Registry (ID: ACTRN12609000913279).