Purposes: The purpose of this study was to evaluate a three-dimensional, virtual reality system for vestibular rehabilitation in patients with intractable Ménière’s disease and chronic vestibular dysfunction. Methods: We included 70 patients (36 for study, 34 as control) with a chronic imbalance problem caused by uncompensated Ménière’s disease. The virtual reality vestibular rehabilitation comprised four training tasks (modified Cawthorne–Cooksey exercises: eye, head, extension, and coordination exercises) performed in six training sessions (in 4 weeks). Measurements of the task scores and balance parameters obtained at the baseline and after final training sessions were compared. Results: A significant improvement was observed in extension and coordination scores. Patients in the early stages of Ménière’s disease had a significantly greater improvement in the center of gravity sway and trajectory excursion in the mediolateral direction than did patients in the late stages of Ménière’s disease. Mild functional disability attributable to Ménière’s disease was a predictor of improvement in the statokinesigram and maximum trajectory excursion in the anteroposterior direction after rehabilitation. The control group showed no significant improvement in almost all parameters. Conclusion: Virtual reality vestibular rehabilitation may be useful in patients with Ménière’s disease, particular those in the early stages or having mild functional disability.