The combination of cerebellar degeneration, hypogonadotropic hypogonadism and chorioretinal dystrophy defines Boucher‑Neuhäuser syndrome (BNS), which has been associated with autosomal‑recessive mutations in the patatin‑like phospholipase domain containing 6 (PNPLA6) gene. However, no BNS cases have been reported in mainland China. In the present study, to the best of the authors' knowledge, the first patient with BNS was identified in China. A 39‑year‑old male was first diagnosed with hypogonadotropic hypogonadism. The proband additionally exhibited retinal degeneration and cerebellar dystrophy. Whole exome sequencing identified a compound heterozygous mutation in PNPLA6 (c.3386G>T+ c.3534G>C). The mutant amino acids were highly conserved and the mutations were predicted to be deleterious. This result further confirmed the role of PNPLA6 in BNS and suggested that whole exome sequencing may be applied for the diagnosis of complex syndromes, including BNS, prior to the observation of obvious symptoms.