The most widely applied algorithm for human papillomavirus (HPV) detection in formalin-fixed, paraffin-embedded (FFPE) specimens of oropharyngeal squamous cell carcinoma consists of p16INK4A immunostaining followed by PCR-based detection of high-risk HPV DNA on the p16INK4A-immunopositive samples. However, in nonoropharyngeal head and neck squamous cell carcinoma (HNSCC) this algorithm fails, hampering correct interpretation of the prevalence and prognosis of HPV in these cases. In this study, we developed and validated a molecular HPV detection method for FFPE specimens of oropharyngeal and nonoropharyngeal HNSCC. Sectioning of the FFPE blocks was circumvented by using punch biopsies from tumor-enriched regions of FFPE tissue blocks, and combined extraction was applied to obtain high-quality DNA and RNA from the punch biopsy. Next, PCR-based detection of HPV DNA was performed for 15 high-risk HPV types with subsequent detection of E6 mRNA for validation. The combined DNA/RNA FFPE test of tissue cores (HPV-rTcore assay) was assessed in well-characterized cohorts with known HPV status based on earlier work, that is, a cohort of oropharyngeal squamous cell carcinomas (n = 80) and oral cavity squamous cell carcinomas (n = 25), and reached an accuracy of 97% and 100%, respectively. In conclusion, our method is rapid, simple, and shows an excellent diagnostic performance for detection of HPV type 16. Ultimately, it can be applied for large cohort studies to determine the etiologic fraction and prognostic implication of HPV in nonoropharyngeal HNSCC.