Chemically caged nucleic acids, which comprise a nucleic acid moiety and a synthetic molecular moiety (or "responsive unit") that may be removed by an appropriate chemical stimulus, are valuable for the development of nucleic acid-based therapeutic strategies like prodrugs and medicine delivery systems. Light is one such stimulus, and excellent examples of photocaged nucleic acids have been developed. However, external light sources must be used for this methodology, and this presents problems concerning light penetration and off-target cytotoxicity. In contrast, chemically caged nucleic acids, which respond to chemical stimuli and autonomously modulate their functions without the need for external stimuli, present an alternative strategy for bioapplications. Herein, recent examples of chemically caged nucleic acids are presented, and the current limitations and future challenges encountered in this field are discussed.