To study the protective role of Baicalin on rats thymus with severe acute pancreatitis (SAP). The SAP rats were randomly assigned to the model control, Baicalin treated and Octreotide treated groups. Normal rats were assigned to the sham-operated group. The rat survival rates, pathological changes of thymus, apoptotic indexes and expression levels of NF-kappaB, Bax, Bcl-2, Caspase-3 and P-selectin of all groups were observed and recorded at 3, 6 and 12 h after operation, respectively. Rat survival rates were significantly higher in both Baicalin- and Octreotide-treated groups than those in the model control group at 12 h (P < 0.05). The thymus pathological score was significantly lower in Baicalin treated group than in control group at 3 and 12 h (P < 0.05). The expression of NF-kappaB, Bax and Bcl-2 in thymus tissue was negative in all groups. At 3 h after operation, the staining intensity, positive staining rate and intensity of Caspase-3 protein in the thymuses of the Baicalin treated group were significantly higher than those in the model control group (P < 0.01). At different time points after operation, no marked difference was observed in the staining intensity of P-selectin protein between the Baicalin treated group and the model control group (P > 0.05). At 6 h after operation, the positive staining rate and intensity of P-selectin protein in the Baicalin treated group was significantly lower than those in the model control group (P < 0.05). The apoptotic indexes were significantly higher in treated group than in model control group at 6 h (P < 0.05). Baicalin has a protective role on the thymus of SAP rats, and its effect of decreasing inflammatory mediators level in blood, inhibiting P-selectin expression and inducing apoptosis of thymocytes may involve in the mechanism of its protective role.