An accurate, reliable, and specific method was developed for the quantitative determination of fumonisins B1, B2, B3, and their hydrolyzed metabolites, HFB1, HFB2, and HFB3, in broiler chicken feed and excreta using ultra-performance liquid chromatography combined with tandem mass spectrometry (UPLC-MS/MS). The samples were extracted and diluted for the determination of parent fumonisins. Another portion of the extracted samples was alkaline-hydrolyzed and cleaned using a strong anionic exchange adsorbent (MAX) for the determination of hydrolyzed fumonisins. Chromatographic separation was performed on a CORTECS C18 column (2.1 mm × 100 mm, 1.6 μm) using 0.2% formic acid aqueous solution and methanol with 0.2% formic acid as the mobile phase under gradient elution. The six fumonisins, FB1, FB2, FB3, HFB1, HFB2, and HFB3, were analyzed by tandem mass spectrometry using multiple-reaction monitoring (MRM) mode. The six fumonisins showed good linearity, with relative coefficients of r > 0.99. The limits of quantitation (LOQs) were 160 μg/kg. At the low, medium, and high spiked levels, the recovery of fumonisins in chicken feed and excreta ranged from 82.6 to 115.8%, with a precision (RSD) of 3.9–18.9%. This method was successfully applied to investigate the migration and transformation of fumonisins in broiler chickens.