Scutellariae Radix, the dried root of Scutellaria baicalensis Georgi (Labiatae), was a commonly used traditional Chinese medicine in clinical practice. Baicalin was one of the effective ingredients enriched in Scutellariae Radix. Recent studies revealed baicalin or Scutellariae Radix extract exhibited various pharmacological activities on cerebral functions. In the present study the pharmacokinetic process of baicalin in normal rat blood and cerebral nuclei (cortex, hippocampus, striatum, thalamus and brain stem) was investigated with a newly established reverse-phase HPLC method after intravenous administration of baicalin-enriched Scutellariae Radix extract prepared according to the special protocol. The pharmacokinetic parameters were calculated by the pharmacokinetic program 3P97 and the regulations of baicalin in blood and cerebral nuclei were comparatively analyzed. The results indicated that the distribution of baicalin into brain was a subsequent process and baicalin tends to accumulate in the striatum, thalamus and hippocampus with the exhibition of large area under the concentration-time curve and mean residence time values (p < 0.05). All these pharmacokinetic data of baicalin in blood and cerebral nuclei would be useful to the dosage regime design when baicalin, Scutellariae Radix extract or the prescriptions containing Scutellariae Radix as the main ingredient are prescribed.