The burden of influenza in Africa is substantial and underappreciated. Although surveillance has increased, the medical community's understanding of seasonal influenza vaccine performance remains limited. We did a systematic review, using PRISMA guidelines (PROSPERO CRD42017058107), on the efficacy, effectiveness, and immunogenicity of influenza vaccines in populations within Africa with the aim of identifying key data gaps to help direct future research. We searched Embase, MEDLINE, Global Health database, and Web of Science for published studies from database inception to May 9, 2018. Unpublished studies were identified by searching ClinicalTrials.gov and the Pan-African Clinical Trial Registry, and by contacting experts within the field. Human studies that reported influenza vaccine immunogenicity, effectiveness, and efficacy were included. 1746 articles were assessed and 23 articles were included. Only three of the 23 studies were of high quality and many studies were underpowered. All 23 studies came from only six African countries (16 from South Africa), highlighting the need for data from a broader range of African populations. The majority of studies focused on effectiveness or efficacy against laboratory supported influenza with limited data for severe outcomes. Several factors known to interfere with influenza immunisation, such as malaria, HIV, and malnutrition were under-represented in this Review and require further study. Substantial gaps exist in our understanding of influenza vaccine performance across all WHO high-risk groups in Africa. Filling these knowledge gaps is vital to guide future influenza vaccine policies.