Objective To investigate the relationship of plasma Epstein-Barr virus (EBV) DNA and serum EBV viral capsid antigen antibody (VCA-IgA) and EBV early antigen antibody (VEA-IgA) with therapeutic efficacy and prognosis in patients with nasopharyngeal carcinoma (NPC) with retropharyngeal lymph node metastasis.Methods We retrospectively analyzed 139 cases of NPC patients with retropharyngeal lymph node metastasis. The real-time fluorescent quantitative PCR was applied to detect the plasma EBV DNA level, while enzyme-linked immunosorbent assay was used to determine EBV VCA-IgA and VEA-IgA levels. According to the curative effect, the patients were divided into remission group and progression group, and the changes in the levels of these indexes before and after the treatments were compared. The relationship of the levels of these indexes with the prognosis and overall survival was analyzed, with survival rate calculated via Kaplan-Meier method and prognostic factors analyzed via Cox regression model.Results The concentrations of EBV DNA differed among different T stages, N stages and clinical stages (P < 0.05), while the concentrations of EBV VCA-IgA and VEA-IgA differed among different clinical stages (P < 0.05). However, the concentrations of EBV DNA, EBV VCA-IgA and VEA-IgA did not differ among patients with different age and gender (P > 0.05). The concentration of EBV DNA after treatment was significantly lower than that before treatment (P < 0.05), while there was no significant difference in the levels of VCA- IgA and VEA-IgA antibodies before and after treatment (P > 0.05). The difference in the level of EBV DNA before and after the treatment was different between the remission group and progression group (P < 0.05), while the differences in the levels of VCA-IgA and VEA-IgA antibodies before and after the treatment did not differ between the two groups (P > 0.05). The 4-year overall survival rate was 72.7%, while that of patients in stage T₁, T₂, T₃ and T₄ was 89.5%, 80.8%, 71.4%, and 59.6%, respectively, with statistically significant differences (P < 0.001). The median survival and 4-year survival rates were different among patients with or without distant metastasis, disease progression or relapse (P < 0.05). Multivariate analysis with Cox regression model showed that clinical stage [R = 2.162 (95% CI: 1.13, 3.215)], EBV DNA level [R = 2.324 (95% CI: 1.242, 5.529)], and the number of cervical lymph node metastases [R = 3.012 (95% CI: 0.653, 5.564)] were risk factors for the survival rate of NPC patients.Conclusions EBV DNA, VCA-IgA and VEA-IgA can be helpful for efficacy evaluation, prognosis estimation, and individualized treatment of NPC with retropharyngeal lymph node metastasis.