Familial neurohypophyseal diabetes insipidus is a rare genetic disease caused by gene variants and is characterized by progressive polyuria and polydipsia in early childhood. Herein, we have reported the clinical symptoms and genetic test results of a Japanese patient with a family history of polyuria and polydipsia for over five generations. The proband was a 6-yr-old boy who was referred for the evaluation of polyuria and polydipsia. A hypertonic saline infusion test showed no increase in AVP levels and a water deprivation test followed by vasopressin administration confirmed the diagnosis of central diabetes insipidus. Genetic analyses of the patient and his affected mother revealed a novel heterozygous missense variant (c.308T>A, p.V103D). This variant was located in the region encoding the neurophysin II moiety. Computational analysis predicted that p.V103D is pathogenic, and a structural change was detected by viewing the three-dimensional structure of the protein model. To our knowledge, this is the first study to identify a novel missense variant, p.V103D, in a Japanese family with central diabetes insipidus. These findings expand the panel of variants and facilitate the genetic diagnosis of familial neurohypophyseal diabetes insipidus.