Background Behçet’s disease is a rare immune-mediated disorder that can affect the gastrointestinal tract. The prevalence and extension of small bowel involvement is largely unknown. Objective The aim of this study was to describe the small bowel lesions diagnosed by double-balloon enteroscopy (DBE) and to verify if these findings were associated to the presence of gastrointestinal symptoms and disease activity after long-term follow-up. Methods This study included 19 Behçet’s disease patients who underwent DBE. After a mean follow-up of 15 years the endoscopic findings were associated to the presence of gastrointestinal symptoms, disease activity and current therapy through collection of electronic medical records. Results A total of 63.2% patients were female and the mean age was 37 years at the time of DBE. Mean disease duration at baseline was 24 years. 11 patients had no gastrointestinal symptoms and eight patients presented either abdominal pain, gastrointestinal bleeding or diarrhea. The average procedure time was 1 hour and 30 minutes and the ileum was achieved in all patients but one. Small bowel ulcers were diagnosed in 78.9%, with 63.1% of jejunal involvement. Two patients presented only small bowel edema and two were normal by DBE. Eight patients had concomitant gastric ulcers. Gastrointestinal symptoms prior to DBE were present in 36.8% of the patients and, after follow-up, all of them persisted with some of the symptoms. Bleeding was reported by three patients at baseline and persisted in only one patient. The frequency of treatment with steroids and immunomodulators was 31.6% and 57.9% at baseline, respectively, and 21% in both at the end of the follow-up. No patient was treated with biologics at the time of the DBE procedure and the current rate of biologic use is 21%. Conclusion Small bowel involvement in Behçet’s disease was frequently demonstrated by DBE even in asymptomatic patients. Understanding clinical evolution of the disease over the years and the impact of such diagnosis still represents a challenge, possibly with the need for novel treatment.