Abstract Background Long-term clinical data on intestinal Behçet’s disease (BD) are scarce because of the rarity of this disease, and many issues remain unresolved due to the difficulty in performing a well-designed clinical trial or epidemiologic study. We aimed to investigate the long-term clinical outcomes of patients with intestinal BD with a 30-year cohort study at a tertiary hospital in South Korea, a hospital with the largest number of patients with intestinal BD worldwide. Additionally, we aimed to identify factors that could predict various clinical outcomes, including anti-tumor necrosis factor-alpha (anti-TNF-α) agent use, intestinal surgery, hospitalization, and emergency room visits. Methods A cohort of 780 patients with intestinal BD between 1997 and 2021 was investigated to determine the long-term clinical outcomes and prognostic factors at the inflammatory bowel disease Clinic of Severance Hospital, Seoul, Korea. Results During the median follow-up period of 12.7 ± 7.2 years, 5-aminosalicylic acids, corticosteroids, immunomodulators, and anti-tumor necrosis factor-alpha (TNF-α) agents were required in 94.9%, 67.2%, 43.8%, and 14.6% of the patients, respectively. The cumulative rates of anti-TNF-α use were 3.7%, 7.5%, 8.5%, 12.1%, 17.6%, and 24.0%, and that of abdominal surgery were 5.7%, 10.9%, 12.6%, 16.5%, 21.6%, and 28.3%, at 1, 3, 5, 10, 20, and 30 years, respectively, after the initial diagnosis of intestinal BD. The cumulative rates of hospitalization were 11.8%, 21.9%, 27.9%, 38.8%, 54.4%, and 74.8% and that of emergency room visits were 10.0%, 19.8%, 22.7%, 31.6%, 50.0%, and 65.0% at 1, 3, 5, 10, 20, 30 years. Older age at primary diagnosis, previous appendectomy history, higher disease activity index for intestinal Behçet’s disease score, systemic BD, multiple intestinal ulcers, deep intestinal ulcers, higher C-reactive protein, lower hemoglobin, and lower albumin levels were associated with poor prognosis. Married status, higher body mass index, oral ulceration, and arthritis were negatively associated with a poor prognosis. Conclusion The data on the long-term clinical outcomes of intestinal BD and their prognostic factors could guide physicians for adequate patient monitoring and optimizing individualized treatments.