Deep penetrating melanocytoma is an uncommon melanocytic tumor characterized by activation of the WNT/β-catenin pathway and can present a diagnostic challenge because of histologic overlap with melanoma and other melanocytic neoplasms. We report a case of WNT-activated deep penetrating melanocytoma arising within a superficial congenital-pattern melanocytic nevus in a 16-year-old male. A slowly darkening, pigmented papule on the left parietal scalp was initially biopsied locally and demonstrated a biphasic compound melanocytic proliferation with a superficial congenital-pattern component and a deeper nested population of pigmented melanocytes. Histopathologic features included rare dermal mitoses, superficial dermal fibrosis, scattered melanophages, and abundant lymphohistiocytic inflammation. Immunohistochemical studies demonstrated MART-1 expression, focal HMB-45 staining, mosaic p16 expression, negative PRAME staining, and nuclear β-catenin staining within the larger central melanocytes. Expert dermatopathology consultation favored a low-grade WNT-activated deep penetrating melanocytoma arising within the congenital-pattern nevus. The lesion extended focally to the specimen base following conservative excision, and close clinical surveillance was selected. This case highlights the importance of recognizing the characteristic biphasic architecture and immunophenotypic features of WNT-activated melanocytoma, particularly when arising within a conventional melanocytic nevus in a pediatric patient. Accurate distinction from melanoma and other melanocytic mimics can help guide appropriate management and avoid unnecessarily aggressive treatment.