We describe a 27-year-old man with mental retardation, symptomatic epilepsy, myopia, and cerebellar ataxia without spontaneous puberty whose brain magnetic resonance imaging showed hypomyelination. He had child-like facial appearance, with thin facial hair. He had no underarm and pubic hairs, and his penis was small. Laboratory tests showed low levels of luteinizing hormone, follicle-stimulating hormone, and testosterone. Brain MRI showed diffuse hypomyelination, atrophy of the cerebellum and brainstem, and hypoplastic corpus callosum. Ictal N-isopropyl-p-(indone-123)-iodoamphetamine single photon emission computed tomography (123I-IMP SPECT) revealed hypoperfusion of bilateral frontal cingulate and temporal lobe and cerebellar hemispheres. Homozygous missense mutation c.2350G>A was found in POLR3A and the patient was diagnosed with Pol III-related leukodystrophy, which is a rare disease. We describe the present case in light of the characteristics of the past reports in Japan. (Received April 5, 2016: Accepted June 30, 2016; Published November 1, 2016).