We report a case of palmoplantar lichen planus in a 7-year-old Japanese girl with congenital deafness, who presented with erythematous eruptions and hyperkeratosis, with peeling and fissures on her soles, palms and digits. On histological examination of a skin biopsy from the lesion on her wrist, lichen planus was identified. Using computed tomography of the inner ears, bilateral cochlear dysplasia was found. The patient’s DNA was sequenced; no sequence variants were detected in the GJB2 gene encoding connexin-26, but she had a missense mutation in SLC26A4 (solute carrier family 26, member 4). Mutations in SLC26A4 are known causes of hearing loss, but this is a novel mutation, which has not been reported previously. In addition, there have been no reports of cutaneous symptoms in previously reported patients with mutations in SLC26A4. To our knowledge, therefore, this is the first report of palmoplantar lichen planus associated with sensorineural deafness accompanied by a mutation in the SLC26A4 gene.