As a naturally occurring amino acid, selenocysteine (Sec) plays a key role in a variety of cellular functions and Se-enriched foods. In this work, a robust water soluble fluorescence turn-on near-infrared (NIR) sensor NIR-Sec was constructed for Sec detection over biothiols in Se-enriched foods. Specifically, NIR-Sec contains a readily prepared water soluble NIR dicyanoisophorone fluorophore and a well-known response-site 2,4-dinitrobenzenesulfonyl moiety with strong intramolecular charge transfer (ICT) effect to quench the fluorescence intensity of NIR fluorophore. Upon addition of Sec, the NIR dicyanoisophorone fluorophore was released and a bright red emission at 663 nm was observed. Moreover, NIR-Sec toward Sec exhibited rapid response time (∼1 min), a large stoke shift (183 nm), and high selectivity and sensitivity (LOD: 52 nM). Impressively, NIR-Sec was successfully employed to detect and image Sec in Se-enriched foods and shrimp, indicating NIR-Sec could provide a robust tool for investigating the role of Sec in complex real-food samples.