X-linked recessive chondrodysplasia punctate (CDPX1) is a rare congenital disorder of bone and cartilage development, is caused by a deficiency of the Golgi enzyme arylsulfatase E (ARSE) gene located on chromosome Xp22.3. It is characterized by punctate calcification in areas of endochondral bone formation, leading to stippled epiphyses, severe nasal and midfacial hypoplasia, short stature, and brachytelephalangy. Here, we present a 4-year-old boy with a rare case of a maternally inherited a 6.4Mb sized deletion on Xp22.33p22.31 identified by SNP array testing. The patient had showed severe significant respiratory compromise caused by extensive punctate calcifications along the tracheobronchial tree during neonate and infant, a right-side hemiplegia, congenital sensorineural hearing loss, delayed cognitive development, short status, typical facial features, and brachytelephalangy. The patient’s mother (recessive carrier) had no clinical problem except smaller expected stature. Our study provides additional information that furthers the understanding and delineation of deletion type CDPX1. To the best of our knowledge, it is the first clinically and genetically confirmed Korean case of maternally inherited deletional type CDPX1.