Intestinal tuberculosis (TB) continues to be a common disease worldwide. However, the optimal duration of anti-TB medication has not been well established. We therefore compared the efficacy of 6-month and 9-month therapy in the treatment of intestinal TB. Ninety patients definitely diagnosed with intestinal TB were randomized into 6-month (n = 45) or 9-month (n = 45) treatment groups, prospectively. The primary end point was complete response, defined as endoscopic healing of active lesions. Patients were followed up monthly for 3 months after therapy initiation, then every 3 months until the end of therapy, and finally 1 year later. Relapse was assessed 1 year after the end of therapy by patient interview and colonoscopy. Baseline characteristics were similar in the 6-month and 9-month groups. Intention-to-treat analysis revealed no significant differences between the two groups in complete response (6-month group, 93.3%; 9-month group, 91.1%; P = 1.00) or recurrence rate (6-month group, 2.4%; 9-month group, 0.0%; P = 1.00). Median follow-up duration was 39 months in the 6-month group and 32 months in the 9-month group. No surgery was performed on any patient in either group. In conclusion, the 6-month therapy was as effective as 9-month therapy in patients with intestinal TB and may have the additional benefits of reduced treatment cost and increased compliance.