Beta-propeller protein-associated neurodegeneration (BPAN) encompasses a group of refractory neurodegenerative diseases that are caused by excessive iron deposition in the brain, especially in the basal ganglia. We reported a case of BPAN with a novel variant of the WDR45 gene at Xp11.23. Our patient was a 31-year-old woman who has had an intellectual disability since childhood. Approximately 3 years ago, she developed asymmetric parkinsonism affecting the distal right upper and lower limbs. Consistent with her neurological findings, dopamine transporter single-photon emission computed tomography demonstrated the differences between the left and right sides. She was diagnosed as BPAN according to genetic analysis, which showed a novel heterozygous variant (c.345-3C>G) in WDR45. To the best of our knowledge, only a few previous case reports on asymmetric BPAN have described the quantitative differences in neuroimaging parameters between the left and right sides. These neuroimaging features were similar to those of Parkinson's disease, among the other neurodegenerative diseases. Our report may provide clues to elucidate the pathological mechanism of BPAN which is a refractory neurodegenerative disease.