Objective To detect the expression of RNA-bound myocardin-related transcription factor A (MRTF- A)-binding genes using RIP-Seq technology in a mouse middle cerebral artery occlusion (MCAO) / reperfusion model and explore the potential mechanism of action of MRTF-A. Methods C57BL/ 6 mice were randomly divided into the sham and cerebral ischemia / reperfusion (I/ R) injury groups. The model of focal MCAO was constructed using the suture method. After 24 h of reperfusion, total brain tissue protein was extracted. Furthermore, the expression profile of MRTF-A-binding genes was detected using immunoprecipitation plus high-throughput sequencing. Additionally, the differentially expressed genes were analyzed using GO and KEGG. Results Compared with the findings in the sham group, 429 genes were differentially expressed (203 upregulated and 226 downregulated genes) in the cerebral I/ R group. GO molecular function analysis revealed that the differentially expressed genes were mainly enriched in RNA binding and Poly(A) RNA binding. KEGG pathway analysis illustrated that 10 pathways were significantly enriched, among which the estrogen signaling pathway was most enriched. Conclusions The expression profile of MRTF-A-binding genes was significantly altered by cerebral I/ R injury, which provides a theoretical basis for in-depth exploration of the molecular mechanism of MRTF-A.