Many patients with intestinal Behçet's disease (BD) still suffer from gastrointestinal symptoms despite the disease being in endoscopic or radiological remission. Previous studies report that small intestinal bacterial overgrowth (SIBO) can be associated with inflammatory bowel disease. However, there have been no reports about SIBO in patients with intestinal BD. We sought to identify the frequency of SIBO in patients with inactive intestinal BD by hydrogen breath test (HBT) and to investigate the efficacy of rifaximin as a treatment for SIBO. Twenty-five patients with intestinal BD who had gastrointestinal symptoms even in endoscopic or radiological remission status were enrolled between January 2012 and January 2016. The patients filled out a questionnaire regarding their subjective gastrointestinal symptoms and took an HBT. Patients with positive HBT results were recommended to take 800-mg rifaximin daily for 14days. Nine patients (9/25, 36%) had a positive HBT test. Eight (8/9, 88.9%) were women, and their mean age was 48.7years. The most common symptom was abdominal distension (8/9, 88.9%), followed by abdominal discomfort (6/9, 66.7%). Rifaximin was prescribed to the nine patients with positive HBT, but two patients refused to take the medication. Four weeks later, six of the seven patients taking rifaximin (85.7%) reported symptom improvement, and none of them reported adverse events. More than one-third of the patients with inactive intestinal BD who had gastrointestinal symptoms were accompanied by SIBO using HBT. Rifaximin might be an effective and safe drug to treat these patients.