Background This retrospective cohort study investigated the economic impact of implementing a nurse-led inflammatory bowel disease (IBD) advice-line and virtual clinic on the Australian healthcare system. The advice line is a telephone and email service managed by IBD specialist nurses. The virtual clinic is a planned, formal communication between the gastroenterologist and the specialist IBD nurse the result of which is communicated to the patient electronically Methods Advice line telephone calls and virtual clinic consultations registered between 1 June 2015 and 1 June 2016 were reviewed and analyzed in terms of outcome: avoidance of general practitioner (GP) consultation, IBD outpatient consultation, emergency department (ED) presentation, or hospital admission. Cost-benefit analysis was conducted to estimate financial savings. Results During the study period, 220 calls were received through the advice line and 1017 virtual clinic consultations occurred. The advice line resulted in the avoidance of 53 GP visits, 159 IBD outpatient department visits, six ED presentations, and one hospital admission. The virtual clinic resulted in the avoidance of four GP visits, 954 IBD outpatient department visits, and 58 ED presentations. This led to an estimated annual cost saving of AUD 169 376.80, with the annual costs incurred estimated to be $58 713. Thus, the annual net benefit of implementing the advice line and the virtual clinic was estimated to be $110 663.80. Conclusion Specialized-IBD-nurse-led advice line and virtual clinic improves IBD patients’ access to services and reduces healthcare costs. This highlights the importance of a proactive multidisciplinary approach in optimizing the care of patients with IBD.