Ischemic stroke (IS) is a neurological dysfunction caused by the avascular necrosis of brain tissues, and its development and progression are the result of both genetic and environmental factors. MicroRNA (miRNA) regulates gene expression at the post-transcriptional level through pairing with the 3'-untranslated region (3'-UTR) of the target gene mRNA, which leads to degradation or translation inhibition of the target gene mRNA. Single nucleotide polymorphisms (SNPs) in the miRNA target regions of IS-related genes are associated with genetic susceptibility and prognosis of IS. This article reviews the association between the SNPs in the 3'-UTRs of miRNA target genes (VEGF, IL-1, NLRP3, MTHFR, PON1, BDNF, CRP, and HDAC9) and genetic susceptibility and prognosis of IS.