Objectives: We propose a novel technique to remove the matrix of cholesteatoma endoscopically after completely filling the mastoid cavity with saline water by perfusion for the appropriate management of labyrinthine fistulas. This “underwater” endoscopic ear surgery (UWEES) technique provides a clear operative field without requiring suction and protects the inner ear from unexpected aeration that may damage its function. Methods: A 3-year-old boy was diagnosed with congenital cholesteatoma in a group medical examination. Once the surgery was scheduled but suspended due to the Great East Japan Earthquake. At the age of 6 years, computed tomography revealed a fistula of the superior semicircular canal and surgery was performed for removal of the cholesteatoma and closure of the fistula. Retroauricular incision was chosen because of the extensive lesion, using an intact canal skin method with soft wall reconstruction. The cholesteatoma was extirpated except for the island lesion of the matrix over the fistula under the operating microscope. Subsequently, saline solution was infused into the mastoid cavity using Endo-Scrub (Medtronic). The island residual matrix was exfoliated underwater endoscopically and closed with bone paste and covered with the fascia. Results: No particular complication occurred during the surgical procedure or postoperatively. Conclusions: Saline water perfusion cleared the surgical field and prevented refraction effects in the high-definition endoscope, resulting in a clear surgical field and prevention of deterioration of cochlear function. UWEES is expected to prevent risk to inner ear function in other interventions such as cochlear implantation, stapes surgery, and temporal bone destruction corrective surgery.