Basaloid squamous cell carcinoma is an infiltrative and aggressive variant of squamous cell carcinoma with basaloid features. Primary skin-derived basaloid squamous cell carcinoma is rare. Basaloid squamous cell carcinoma is commonly observed in the oropharyngeal and anogenital regions and is associated with high-risk human papillomavirus. We report a case of primary basaloid squamous cell carcinoma overlying the right scapula with metastasis to the regional lymph nodes and brain despite surgical resection and adjuvant chemoradiation. Histopathologic investigations of high-risk cutaneous squamous cell carcinoma do not routinely involve human papillomavirus testing. In contrast, oncogenic human papillomavirus and p16 are screened in head and neck squamous cell carcinoma for prognostication. Since the patient presented with an aggressive variant of squamous cell carcinoma and distal metastasis despite standard therapies, human papillomavirus testing was performed. P16, a surrogate marker for human papillomavirus infection and specifically HPV16 was identified in the tumor. This is a unique report of HPV16 in primary cutaneous basaloid squamous cell carcinoma with distal brain metastasis.