We developed a simple and sensitive HPLC method for the determination of selenocyanate (SeCN⁻). The König reaction, which is generally used for the determination of cyanide and thiocyanate, was applied for the post-column detection, and using barbituric acid as a fluorogenic reagent made it possible to detect SeCN⁻ with high sensitivity. The limits of detection (LOD) and quantification (LOQ) were 73.5 fmol and 245.1 fmol, respectively. Subsequently, the amounts of SeCN⁻ in human blood and in cultured cell samples were analyzed, and no SeCN⁻ was detected in human whole blood. Interestingly, we have found that some of the spiked SeCN⁻ decomposed to cyanide in human whole blood. Ascorbic acid suppressed the decomposition of SeCN⁻ to cyanide by reducing the ferric ion, which is typically involved in SeCN⁻ decomposition. Then, SeCN⁻ was detected in cultured HEK293 cells exposed to selenite. The established HPLC method with fluorescence detection of SeCN⁻ is useful for investigating small amounts of SeCN⁻ in biological samples.