The study highlights the effect of ethylacetate subfraction F1 from Polygonum cuspidatum root and piceid on the inhibition of Epstein-Barr virus (EBV) lytic gene expression. The MTT [3-(4,5-dimethyldiazol-2-yl)-2,5-diphenyltetrazolium bromide] method was employed to assess the effect of F1 and piceid on the cell survival of P3HR1. The immunoblotting method and flow cytometry were applied to analyze the expression of EBV lytic proteins. The results showed that the EC50 (effective concentration required to inhibit 50% EBV lytic proteins) of F1 and piceid inhibiting the lytic proteins of EBV were 23.3 μg/mL and 119.6 μM, respectively. For P3HR1 cytotoxicity, the CC50 (cytotoxic concentration that decreased cell viability by 50%) of F1 and piceid were 93.1 μg/mL and 507.9 μM, respectively. In other words, F1 and piceid effectively inhibited the expression of EBV lytic proteins at a non-cytotoxic concentration. qPCR was performed to analyze the effect of F1 and piceid on the transcription of lytic genes, including BRLF1, BZLF1, and DNA replication of EBV. The results showed that F1 and piceid inhibited the transcription of lytic genes and reduced DNA replication of EBV with EC50 of 55.5 μg/mL and 89.9 μM, respectively. The results of this study confirmed that F1 and piceid could effectively inhibit the expression of EBV lytic proteins and EBV DNA replication, indicating that F1 and piceid are potentials for use as anti-EBV drugs.