The Epstein-Barr virus encoded nuclear antigen 1 (EBNA1) is required for the replication and maintenance of the episomal EBV genome and for the transactivation of viral gene expression. EBNA1 has been classified into five subtypes, among which the V-val subtype was reported to be associated with nasopharyngeal carcinoma (NPC). Here we report a higher transcriptional activity of the V-val subtype of EBNA1 than for the prototype derived from B95.8 cells to transactivate FR-containing luciferase plasmid, which was mainly a consequence of the mutations in the carboxy-terminus of EBNA1. This interpretation was further supported by the finding that the variant form of EBNA1 has a higher binding affinity for the FR sequence than the prototype by electrophoretic mobility shift assays. The functional advantage of the V-val EBNA1 investigated in this study may contribute to the oncogenesis of NPC.