Vulvar squamous cell carcinoma (VSCC) can be classified according to human papillomavirus (HPV) status as HPV-associated (HPV-A) and HPV-independent (HPV-I). However, a small subset of tumors may show overlapping features and become a serious diagnostic challenge for pathologists. We report an unusual case of VSCC arising in a 21-year-old patient with type 1 diabetes mellitus. The tumor had keratinizing histologic features, was associated with a premalignant lesion with features of a high-grade squamous intraepithelial lesion (HSIL), and showed consistent p53 immunohistochemical (IHC) overexpression, but variable results in the HPV testing and p16 IHC staining. Molecular analysis revealed mutation of TP53 and overexpression of cell cycle-regulating genes (including CCND1) and collagen-coding genes (such as COL6A1). These molecular findings in genes, previously reported as upregulated in HPV-I VSCC, supported an etiological origin independent of HPV for the tumor. In conclusion, molecular analysis may help to correctly classify challenging VSCC, showing puzzling clinical, morphologic, and IHC characteristics.