Objectives Surgical management of cholesteatomas with labyrinthine fistulae has been reported and several techniques have also been advocated, however, no uniform surgical technique can be adopted in all cases with fistulae. We examined the efficacy of MRI evaluation for surgical management of cholesteatoma with a labyrinthine fistula. Methods The case histories of 23 patients who had undergone surgery for middle ear cholesteatoma with a labyrinthine fistula were examined. Imaging analysis was performed using a 3-dimensional fluid-attenuated inversion recovery (3D-FLAIR) magnetic resonance imaging (MRI) sequence. Clinical symptoms, presence of fistulae, surgical management, and postoperative outcomes were compared between groups who had or had not undergone preoperative 3D-FLAIR MRI. Results Safe surgical management was achieved in the group without MRI evaluation. The group with MRI evaluation contained cases with larger fistulae and more severe clinical symptoms; however, MRI provided precise information concerning the degree of labyrinthitis, which enabled adequate surgical management and successful outcomes including improvement of sensorineural hearing loss in some cases. Conclusions Information provided by 3D-FLAIR images is valuable in the surgical management of cholesteatoma with a labyrinthine fistula, especially in cases with large fistulae and severe symptoms related to inner ear disturbances.