This study demonstrated a novel method using online post-column derivatization high-performance liquid chromatography (PCD-HPLC) to evaluate selenocysteine (SeC) in Se-enriched yogurt. The liquid chromatography process utilized a C18 column. The mobile phase A was composed of 4.0 mM borate buffer adjusted to pH 5.0, while mobile phase B was a 50:50 (v/v) mixture of methanol and acetonitrile. The mobile phases were combined at a ratio of 70:30, with a flow rate of 1 mL min−1. SeC was derivatized to bis-Fmoc selenocystine after separation, using a PCD solution (0.03 mM Fmoc, pH 10, 20 mM borate buffer, and 1.0 mL min−1 flow rate) and detected with a photodiode array detector (DAD) for sensitivity enhancement. The method exhibited excellent linearity (0.023 to 0.20 mg L-1, r2 = 0.9996), with a low LOD and LOQ of 0.018 mg L-1 and of 0.040 mg L-1, respectively. Repeatability and reproducibility were satisfactory, with recoveries of 95.50 % ± 1.49 % (the proposed PCD-HPLC) and 94.33 % ± 0.44 % (sample preparation). This method effectively analyzed the conversion of selenite ions (SeO32-) to SeC by lactic acid bacteria in yogurt, highlighting Se-enriched yogurt as a valuable dietary source of SeC. However, the synthesis efficiency of SeC decreased at inorganic Se supplementation levels above 1.0 mg Se L-1, potentially leading to the formation of less toxic elemental Se (Se0). Therefore, the proposed online PCD-HPLC method proves reliable for SeC analysis in Se-enriched yogurt, providing insights into Se speciation and optimizing Se enrichment processes.