Fewer studies have been done over the years to establish the association of human papillomavirus (HPV) with head and neck squamous cell carcinoma (HNSSC) within the subregions of sub-Saharan Africa, and thus this study was designed to investigate the presence of HPV in HNSCC at a tertiary hospital in Ghana, providing additional evidence on the need to explore similar studies in other subregions. A retrospective cross-sectional study was employed to investigate the presence of the DNA of HPV genotypes in HNSCC archived tissue. A total of 100 HNSCC cases were classified as suitable for HPV genotyping. HPV-DNA was detected in 18% of the HNSCC cases, with 17 being HPV-16 and 1 dual infection with HPV-16 and HPV-18. HPV was prevalent in 50% of oropharyngeal cancers, 27% of laryngeal cancers, and 23% of oral cavity cancers. HPV E6/E7 oncogenic DNA was found in 18% of the HNSCC cases, with HPV-16 being the predominant genotype present. The pattern of HPV association was similar to earlier reported studies, recording a higher prevalence in oropharyngeal cancers, followed by laryngeal cancers and oral cavity cancers.