Background: The traditional Chinese medicine Scutellariae radix is often used in combination with antibiotics, such as florfenicol, in Chinese veterinary medicine. Baicalin (5, 6, 7-trihydroxyflavone-7-β-D-glucuronide) is the main active constituent of S. radix. The effects of baicalin on the pharmacokinetics of florfenicol are not known. Thus, we have studied the effects of baicalin on florfenicol pharmacokinetics and the mRNA expression of drug-metabolizing enzymes/efflux transporters in rats. Materials and Methods: Sprague-Dawley rats were given baicalin (50 mg/kg BW or 100 mg/kg BW) or 0.9% sodium chloride solution by intragastric administration for 7 days. They were then fed florfenicol by intragastric administration (25 mg/kg BW) on the 8th day. Blood samples were collected at various times, and the plasma concentrations of florfenicol were estimated with ultra-high performance liquid chromatography. The mRNA expression levels of cytochrome P450 (CYP) CYP1A2, CYP2C11, CYP3A1, UDP-glucuronosyltransferase 1A (UGT1A), multidrug resistance 1, and ATP-binding cassette C2 (ABCC2) in the liver and jejunum were analyzed with a real-time polymerase chain reaction. Results: The area under the concentration-time curve from zero to infinity, mean residence time from zero to infinity, elimination half-life, and peak concentration of florfenicol were significantly increased and the apparent volume of distribution fraction of the dose absorbed and plasma clearance fraction of the dose absorbed were significantly decreased by baicalin; the mRNA expression levels of CYP1A2, CYP2C11, CYP3A1, UGT1A1, and ABCC2 were down-regulated by baicalin. Conclusion: Baicalin affected the pharmacokinetics of florfenicol in rats, increased the plasma concentration and residence time of florfenicol, probably by decreasing the mRNA expression levels of CYP1A2, CYP2C11, CYP3A1, UGT1A1, and ABCC2 in the liver and jejunum.