Facial nerve stimulation (FNS) is a side-effect of cochlear implantation that can result in severe discomfort for the user and essentially limits the optimal use of the implant. Three-dimensional cochlear implant modelling research has led to the progression from generic models to user-specific models with one of the intentions to develop model-based diagnostic tools. The objective of this study is to investigate the mechanisms that underlie the manifestation of FNS in the post-meningitic cochleae of a specific CI user through computational modelling. Bilateral models were created using a method previously developed for the construction of a three-dimensional user-specific volume conduction model of the cochlea and was expanded to include the facial nerve geometry. Reduced temporal bone density based on bone densitometry, cochlear duct ossification and degenerate auditory neural fibres were incorporated into a comprehensive FNS model. Auditory and facial nerve thresholds were predicted with the models showing good correspondence to perceptual thresholds and the user's FNS experience. Ossified cochlear ducts appear to aggravate the increase in thresholds caused by the otic capsule's decreased resistivity. This translational case study demonstrates the application of computational modelling as a clinical instrument in the assessment and management of complications with cochlear implantation.