Objective To compare the cost-effectiveness of Baofukang and Xinfuning in the treatment of HPV infection, and to provide references for reasonable clinical prescription, pricing drugs and the cognition product value. Methods Decision tree model was developed to estimate the cost-effectiveness of Baofukang and Xinfuning from the perspective of the cost payer. In the model, the effectiveness was mainly measured by the clearance rate of HPV based on meta-analysis. The cost data was mainly based on the published price data from the websites of the Development and Reform Commission, Bidding Center, the Health Department and so on. The single factor sensitivity analysis was performed based on the change of effectiveness and price. Results The effective rate of Baofukang treatment for 48 days was 61.89%, and the effective rate for 42 days was 63.05%, while Xinfuning’s effective rate for 30 days was 46.58%. The total cost were 668.61 yuan, 630.09 yuan and 850.83 yuan, respectively. Baofukang users had lower costs yet higher clearance rates of HPV compared to Xinfuning at different treatment time. In sensitivity analysis, the evaluation results would not been affected. Conclusion The current study suggests that Baofukang is more cost-effective than Xinfuning in the treatment of HPV infection.