The aim of this study was to determine the prevalence of facial nerve (FN) bifurcation in patients who undergo stapes surgery, and to ascertain the correlation between the intraoperative and radiographic findings in cases where an unexpected branch malformation for patients undergoing stapes surgery. Patients who underwent stapes surgery were retroactively examined for confirmed FN bifurcation. Among the 887 patients, 10 had a bifurcated FN confirmed during surgery and had a preoperative high-resolution computed tomography (HRCT) scan. The HRCT scans were examined by two radiologists who were blinded to the operational findings. The diagnostic accuracy of HRCT imaging was examined along with their preoperative audiometry. In total, 887 patients underwent stapes surgery and among them the prevalence of FN bifurcation was 1.13%. These 10 patients had a 1:1 male-female ratio with a mean age of 17.9 ± 7.0 years. From a surgical review, all cases had bifurcation at the horizontal segment of FN, including 1 case of FN trifurcation. The diagnostic difference between HRCT imaging and intraoperation observations for malformations in the middle ear varies widely depending on the location, ranging from 0% to 90%. The prevalence of incus and stapes malformations was high in both imaging and operation findings (≥60%). The detection rate of abnormal positioning and bifurcation of the FN during HRCT imaging was 30% and 0%, respectively. The mean air-bone gap hearing threshold for patients was significantly improved from 42.3 dB preoperatively to 15.6 dB postoperatively without any complications. These results showed that it is extremely difficult to predict the FN bifurcation prior to surgery with a detection rate of 0%. The diagnostic difference between HRCT imaging and intraoperation observations for malformations of different parts of the middle ear varies widely. These results highlight the importance of being vigilant in regard to FN anatomical variation during stapes surgery for any unexpected malformations that are not detected during HRCT evaluation. In addition, the surgical outcomes for these patients were optimal when treatment was performed by senior surgeons.