Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare hematologic neoplasm derived from plasmacytoid dendritic cell precursors. The malignancy was characterized by cutaneous and bone marrow involvement and leukemic spread，predominantly involving elderly patients. Pediatric cases of BPDCN are much fewer reported in the literature, making the management of pediatric BPDCN challenging. We report a congenital BPDCN patient who manifested with neutropenia and nodular skin lesions. Whole-exome sequencing suggests the presence of kmt2c gene duplication. She died four months after diagnosis. This case report reminds clinicians, especially neonatologists, to consider the possibility of BPCDN when finding neonates present with rash(such as purplish nodules, bruiselike macules) and a cytopenia. In addition, this study suggests that the KMTC2 gene may play a vital role in the pathogenesis of BPDCN.