Scutellarin (SG) is a bioactive flavonoid used to treat cardiovascular disease. Scutellarein (S) is the aglycone form of SG. This study aimed to characterize their intestinal transport and first-pass metabolism by UDP-glucuronosyltransferase-mediated glucuronidation and β-glucuronidase-mediated hydrolysis. Results showed that S is more readily passed through Caco-2 cell monolayers by passive diffusion than SG. SG was the predominant metabolite of S, which was formed during the transportation of S across Caco-2 cell monolayers or following incubation of S with human microsomes. SG was extensively generated in human liver microsomes (HLMs), which was demonstrated by its higher catalyzing efficiency (C(lint)) in liver microsomes than in human intestinal microsomes (HIMs). Enzymatic kinetic analysis indicated that the catalyzing efficiency of UGT1A9 was the highest among the tested UGTs under the present experimental conditions, followed by UGT1A1 and UGT1A3. No significant P450-mediated hydroxylation of S was found. SG may be hydrolyzed into S in both HLMs and HIMs.