Context: Alzheimer’s disease (AD) is a neurodegenerative disease affecting many people around the world. Recently, it has been reported that toll-like receptors (TLRs) play a role in AD; therefore, the present study aimed to systematically review the studies and to meta-analyze the role of toll-like receptor 9 (TLR9) in AD. Methods: Seven main electronic databases, including PubMed/MEDLINE, Web of Science, Embase, Scopus, CINAHL, Cochrane, and Google Scholar, will be considered with no language restrictions. Full texts of articles will be prepared by a determined search strategy. Studies including the assessment of TLR9 function in adults with AD, published before June 15 2020, will be considered. Hence, this protocol will be presented based on the preferred reporting items for systematic reviews and meta-analyses (PRISMA) statements for protocols. The related results and data analyses will be provided in the final review. This paper plans the protocol for a systematic review identifying TLR9 up-regulation and down-regulation in adults with AD. Conclusions: The meta-analysis of TLR9 may subsequently provide attractive therapeutic tools for AD.