Advanced systemic mastocytosis with associated hematologic neoplasm (SM-AHN) is a rare, genomically unstable disorder with a high risk of clonal evolution. We report a 74-year-old man with SM-AHN (chronic myelomonocytic leukemia subtype) harboring KRAS, RUNX1, SRSF2, and TET2 mutations who was treated with avapritinib, hypomethylating therapy, and matched-unrelated donor allogeneic stem cell transplantation. Nine months post-transplant, he developed a violaceous cutaneous lesion. Histopathology and immunophenotyping confirmed blastic plasmacytoid dendritic cell neoplasm (BPDCN). Next-generation sequencing of the lesion revealed shared SRSF2 and TET2 mutations with the antecedent CMML clone and acquisition of a novel GNB1 mutation, supporting clonal evolution under treatment-related selective pressure and post-transplant immune modulation. Diagnostic distinction from mastocytosis relapse, leukemia cutis, and graft-versus-host disease requires integrated morphologic, immunophenotypic, and molecular evaluation. Treatment with CD123-directed tagraxofusp was complicated by severe capillary leak syndrome, and the patient passed away following re-challenge, underscoring the substantial risk this therapy carries in heavily pretreated, post-transplant patients. BPDCN may represent a late manifestation of clonal progression after allo-HSCT, emphasizing the importance of longitudinal molecular monitoring and vigilance for new cutaneous lesions in post-transplant patients with SM-AHN.