Background: Epstein-Bar virus (EBV) is reported to be intimately associated with the development of nasopharyngeal carcinoma (NPC), the most common and high incidence cancer of the head and neck in Asian countries. Among the EBV DNA genome, the EBNA-1 gene plays an important role in NPC. Objective: a meta-analysis was performed according to the PRISMA guideline to systematically evaluate the association between the EBNA-1 and NPC. Materials and methods: Relevant articles were identified by searching the MEDLINE database. The frequency and Odds ratio (OR) were applied to estimate the effect of EBNA-1 based on random-/fix-effects models. Results: eight studies included 1,372 samples: 588 samples from NPC cancer patients, and 784 samples from non-cancerous samples, were enrolled in the meta-analysis. The overall frequency of EBNA-1 in NPC patients and controls was 88.72% and 4.32%, respectively. The current meta-analysis suggested that individuals with the presence of EBNA-1 are associated with NPC risk under the fix-effects model (pooled OR = 331.09, 95%CI = 139.95-783.30). Our findings underscore the correlation among EBNA-1 and all subgroups, including region, method, and source of samples under the fix-effects model. Conclusion: Based on those findings, the presence of EBNA was suggested as a promising biomarker for the diagnosis and screening of NPC.