Scutellarein, which is the main metabolite of scutellarin in vivo, has better neuroprotective effects than scutellarin against brain ischemia. However, there are few studies on the metabolic profile of scutellarein in vivo. In this study, a method based on ultra performance liquid chromatography/quadrupole-time-of-flight mass spectrometry was applied to identify the scutellarein and its metabolites in rat plasma, urine and feces after oral administration of scutellarein. Using MS^E and mass defect filter techniques, scutellarein (M1), the glucuronide conjugate of scutellarein (M2, M3), scutellarin (M4), 6,7-di-O-β-D-glucuronide scutellarein (M5), the glucuronide conjugate of apigenin (M6), 4′-O-sulfate scutellarein (M7), the methylated conjugate of scutellarein (M8), the methylated and glucuronide conjugate of scutellarein (M9), and the acetylated conjugate of scutellarein (M10) were detected in rat urine. M1, M2, M4, and M10 were detected in rat plasma and only M10 was found in feces. Our studies indicated that scutellarein can be metabolised by glucuronide conjugation, dehydroxylation, sulfation, methylation and acetylation in vivo after oral administration.