Chromatin immunoprecipitation (ChIP) was performed to analyze EBV histone modification patterns in SNU719 cells treated with cordycepin. Seven EBV genomic loci in the EBV genome—1300 (LMP2), 6926 (between BNRF1 and BCRF1), 11675 (between BCRF1 and BCRF2), 12450 (5′ UTR of BCRF2), 41126 (between BHLF1 and BHRF1), 51251 (BPLF1), and 83382 (EBNA3B)—were detected by RT-qPCR. Cordycepin reduces H3K4me3 histone enrichment at loci 1300, 12450, 41126, and 83382. Similarly, H3K9me3 histone enrichments at loci 1300, 12450, and 83382 were also a little reduced. These results indicate that cordycepin treatment results in histone modification at EBV genomic loci, consequently downregulating EBV genes.