Johanson-Blizzard syndrome is a rare genetic disorder characterised by various systemic manifestations, including sensorineural hearing loss. We present a unique case of a 3.5-year-old girl with genetically confirmed Johanson-Blizzard syndrome, who exhibited typical features alongside rare radiological findings of cystic dilation of the cochlea and hypoplastic modiolus. This report highlights the need for recognising and evaluating unusual radiological abnormalities associated with this syndrome, particularly in cases of sensorineural hearing loss, to guide appropriate interventions. The identification of cochlear anomalies in this case provides essential information regarding the aetiology of sensorineural hearing loss in Johanson-Blizzard syndrome and highlights the necessity for comprehensive assessment and tailored management strategies to improve auditory rehabilitation and overall outcomes in affected individuals.