Ischemic stroke (IS) is a complex disease affected by several environmental factors, genetic factors, and their interactions. Stress disorder (SD) can also independently increase the risk of stroke. Many genetic factors are similarly found in IS and SD. Genetic factors play an important part in the pathogenesis of IS and SD. The identification of genetic factors has become a hot topic for current research. In the investigation described herein, we aimed to identify possible common gene targets and relevant drug molecules in the pathogenesis of IS and SD. The microarray dataset of GSE16561 for IS and GSE125216 for SD were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) of IS and SD were attained using the limma package in R. Only 31 common DEGs overlapped in both datasets. The common DEGs were analyzed by Search Tool for the Retrieval of Interacting Genes online database and Cytoscape software. To predict their interaction relationship with the protein-protein interaction (PPI) network, hub proteins were counted by their node degree value from the PPI network. Functional analysis was also applied, and significant gene ontology (GO) terms were retrieved. Finally, identified common DEGs were submitted to the DSigDB database, and related drug molecules were retrieved. Ten molecules were identified from the common DEGs.