IntroductionHuman papillomavirus (HPV) is an established risk factor for oropharyngeal squamous cell carcinoma, regardless of a history of other known risk factors such as alcohol and tobacco. While cases of HPV-related oral squamous cell carcinoma (OSSC) are increasing in the USA, Europe and South Central Asian countries, little is known about the impact of the disease on the African continent.Methods and analysisWe describe a protocol for a systematic review to synthesise the best current evidence to assess the disease burden in Africa. Electronic databases including EBSCOhost, MEDLINE, CINAHL, ACADEMIC SEARCH COMPLETE, ScienceDirect, Web of Science, Scopus, SciCENTRAL, Cochrane Library, International Prospective Register of Systematic Reviews) and WorldCAT will be comprehensively searched for studies reporting on the defined outcomes, in Africa, published from 1985 (when HPV was first reported) to the latest current entries, with no language restriction. Supplemental handsearching of grey literature, conference abstract proceedings, reference lists of included studies and citations in Google Scholar will be conducted. Authors will be contacted, where necessary, to assist with missing data. A customised data extraction form, with specified criteria, will be used for data extraction. Overall study quality assessment will be done using an appropriate risk of bias tool suited to the study design. Where available, qualitative data from studies reporting on the outcomes will be captured on the data extraction form. Using Stata software, we will apply the random-effects meta-analysis model to aggregate prevalence estimates with 95% CI, incorporating the Freeman-Tukey transformation to account for between-study variability. A narrative report of the findings will be presented where data are insufficient in terms of the outcome/s. Subgroup analysis will be done subject to sufficient available data.Ethics and disseminationEthics approval or written consent is not required as the review will be conducted using published data. The findings will be distributed through a peer-review publication and conference presentation.