Congenital Spitz nevi have been rarely reported, and the diagnoses were usually based on the histopathological and immunohistochemical findings. We describe a case of a congenital Spitz tumor in which the molecular studies demonstrated a ZKSCAN1::MET fusion. No other somatic mutations and/or copy number variations outside of the MET gene were identified. Activating MET kinase rearrangements were previously reported only in a few cases of atypical Spitz tumors and spitzoid melanomas. Specifically, the ZKSCAN1::MET fusion was previously described in a single case of spitzoid melanoma demonstrating an uneventful course. Altogether, the histopathological, immunohistochemical, and molecular studies in our case supported a diagnosis of a congenital Spitz melanocytoma. This underscores the value of molecular analyses in Spitz tumors.