<p>Bone radiodensity and thickness between the cochlear implant’s middle electrodes and the facial nerve were compared across four groups—Facial nerve stimulation (FNS) patients with and without far advanced otosclerosis (FAO), and controls with and without FAO—using manual segmentation of photon counting-computed tomography (PC-CT) to assess FNS risk. This case-control study compared FAO patients with FNS (<i>n</i> = 3) to non-FAO with FNS (<i>n</i> = 2) and two control groups without FNS of post-lingually deafened patients: FAO (<i>n</i> = 2) and non-FAO (<i>n</i> = 2). Clinical data from medical record included surgical details, complications, PC-CT findings (bone thickness between the middle electrodes and the facial nerve), hearing outcomes, and implant fitting at two years. Manual segmentation of PC-CT was performed using ITK-SNAP software to measure the bone radiodensity between the mid-array electrode and the adjacent facial nerve. No significant differences were found between FNS and non-FNS patients in demographics, surgical outcomes, complications, audiometric data, or implant programming at 2 years post-surgery. A significant difference in bone radiodensity was observed in patients with FAO (1483.57 ± 122.37 HU (Hounsfield Units)) compared to those without FAO (2403.51 ± 128.24 HU; <i>p</i> &lt; 0.001). In the non-FAO with FNS group, one patient exhibited an exceptionally short distance (0.13&#xa0;mm) between the first portion of the facial nerve and the middle electrodes. When comparing FNS and non-FNS patients, no significant differences were observed in bone radiodensity (<i>p</i> = 0.85) or in bone thickness (<i>p</i> = 0.75). ITK-SNAP enables manual PC-CT segmentation to assess bone radiodensity and thickness between cochlear implant electrodes and the facial nerve. In otosclerosis, lower radiodensity alone doesn’t explain FNS, but reduced bone thickness may contribute.</p>