Congenital atrichia with papular lesions (APL) is a disease characterized by the complete absence of hair from the whole body occurring within a few months of birth and the presence of papules distributed over the body. A 9-year-old boy presented with sparse hair over his body and with a history of losing his hair soon after birth. Multiple skin-colored papules were observed over the scalp. A biopsy from a papule showed keratinous cysts in the dermis and the absence of hair follicles. A diagnosis of congenital APL was made after vitamin D-dependent rickets was excluded. This case highlights congenital APL as a cause of total alopecia.