Introduction: Foodborne infections are caused by a wide spectrum of microbial pathogens, and they pose a significant global health threat, resulting in millions of cases and thousands of fatalities annually. Among these pathogens, human viruses, including Hepatitis A virus (HAV) and Hepatitis E virus (HEV), play a significant role in foodborne viral outbreaks, especially in Africa. This systematic review determined the prevalence of these viruses in livestock and produce in Africa. Method: A systematic search strategy was implemented following the PRISMA guidelines. Databases such as African Journal Online, Web of Science, Scopus, and PubMed were searched from their inception until November 30, 2023. Descriptive statistics and a proportional meta-analysis utilising a random-effects model with a 95% confidence interval were employed in the data analysis. The Cochrane risk-of-bias tool (ROB2) was utilised to evaluate the potential for bias in each study. Results: The search identified 27 articles that met the inclusion criteria, among which seven focused on HAV, comprising a total of 309 samples, whereas 20 studies focused on HEV, comprising a total of 4238 samples. Egypt had the highest number of studies, followed by Cameroon and Nigeria. The meta-analysis revealed an overall prevalence of 33.8% (95% CI: 17.0–50.6) for HAV in ducks and shellfish and 22.0% (95% CI: 12.1–31.8) for HEV in various livestock. Genotype 3 was identified as the predominant genotype, for both HAV and HEV. Conclusion: This review revealed a high prevalence of HAV and HEV in livestock populations in Africa, shedding light on the potential risks associated with zoonotic and/or food-related infections. There is a need for continued surveillance and monitoring of these viruses in both animals and food products to mitigate the risk of foodborne outbreaks and protect human health.