This presented study describes a method based on high performance liquid chromatography combined with fluorescence detection (HPLC-FLD) using N-(2-iodoacetyl)-1-pyrenemethylamine (NIPA) as a novel fluorescence labeling reagent for the determination of thyreostats in bovine milk. Five thyreostats, belonging to the group of imidazole and thiouracil, were investigated in this work: tapazole (TAP), thiouracil (TU), methylthiouracil (MTU), propylthiouracil (PTU) and phenylthiouracial (PhTU). Thyreostats were specifically purified by a silver ion solid phase extraction (Ag-SPE) cartridge and then labeled using NIPA. The labeled derivatives showed excellent fluorescence property with maximum excitation and emission wavelengths of 330 nm and 375 nm, respectively. The labeled derivatives were separated on a reversed-phase Eclipse SB-C18 column within 12 min. Excellent linearity (R2 > 0.995) of all thyreostats was achieved with the limits of detection (LODs) and the limits of quantitation (LOQs) in the low micrograms per liter range of 0.21–0.30 μg/L and 0.70–1.00 μg/L, respectively. Satisfactory recoveries in the range of 93.5–98.0% were obtained for all thyreostats. The developed method has been successfully applied to analyze thyreostats in bovine milk with good applicability. Thirty bovine milk samples have been investigated, and varying levels of thiouracil were detected in thirteen of these samples. The highest level in the raw milk reached a value of 4.5 μg/L. To our best knowledge, this study is the first to report the presence of naturally occurring thiouracil in milk by HPLC-FLD analysis.