The prevalence of encephalomyocarditis virus has brought about enormous financial losses to the swine industry throughout the globe. Chinese herbal medicines have potential antiviral activity which has been proved. Fifteen traditional Chinese medicine compounds were screened for anti-encephalomyocarditis virus (EMCV) activity. The maximum non-toxic concentration (MNTC), cytotoxic concentration 50% (CC50), maximal inhibition rate (MIR), and effective concentration 50% (EC50) against EMCV were measured using MTT and antiviral assays on baby hamster Syrian kidney (BHK-21) cells. Two of the compounds, baicalin and matrine, with MIR > 50% and selective index (SI) > 3 were chosen for further virus load analysis. The results showed that the MIRs of baicalin and matrine were higher than that of positive control ribavirin while the SI values were much smaller than that of the control. Real-time quantitative PCR analysis demonstrated that baicalin and matrine have significant (p < 0.05) anti-EMCV activity compared to the control. It is a baseline study concluded that baicalin and matrine needs further development as an independent drugs or part of a Chinese medicine prescription for the treatment of EMCV infection.