The discovery of riboswitching has accelerated research on the interaction between RNA and small organic compounds. It will be important for biologists to artificially and reversibly control gene expression in vivo through the interaction of RNA and small molecules. In this paper, we report that RNA aptamers obtained from in vitro selection in which a photoresponsive short peptide containing the azobenzene moiety with flanking arginine residues on both sides as a ligand provided reversible binding to the ligand peptide immobilized onto the gold surface. We designed and synthesized a photoresponsive short peptide that can interact with RNA, can convert its conformation reversibly by photoirradiation, and can be produced on a large scale for in vitro selection. The RNA pool contained N70 random sequences, and after the eighth cycle, we identified RNA aptamers showing the K-d of about a few micromolar. A surface plasmon resonance (SPR) experiment revealed that RNA aptamers could bind to the trans-isomer of the peptide immobilized on the gold surface but not to the cis-peptide isomerized by photoirradiation with 360 nm light to the gold surface. The SPR signals were recovered after photoirradiation with 430 nm light, leading to isomerization of the peptide from cis to trans.