Objective To investigate the clinical features and potential associated risk factors of Epstein-Barr virus (EBV) DNA positivity in systemic lupus erythematosus (SLE) patients. Methods A total of 121 newly diagnosed SLE patients who had never used immunosuppressive drugs (treatment-naive) and 191 previously treated SLE patients from January 2017 to January 2020 were enrolled in this study. And 115 age- and sex-matched non-rheumatic disease controls were also included. Results A significantly higher incidence of EBV DNA positivity and higher viral DNA copies in peripheral blood mononuclear cells were observed among treatment-naive and previously treated SLE patients compared with controls. The positivity rate of EBV DNA was further increased in previously treated SLE patients compared with that in treatment-naive patients. EBV DNA-positive treatment-naive SLE patients presented lower incidence of hemolytic anemia and more affected organ number than EBV DNA-negative patients. EBV DNA-positive treated SLE patients showed older age, longer immunosuppressive duration, higher IgG level, and higher Th/Ts ratio than EBV DNA-negative patients. Patients responding well to treatment with decreased SLE disease activity index scores had a transformation of EBV DNA from positive to negative in treated SLE patients. Multivariate logistic regression analysis showed that older age, higher IgG level, and longer immunosuppressive duration were associated risk factors for EBV DNA positivity in SLE patients, while higher TNF-alpha level was a protective factor. Conclusion Older age, higher IgG level, and longer immunosuppressive duration are associated with the positivity of EBV DNA in SLE patients. A seroconversion of EBV DNA indicates an association between EBV positivity and therapy response, while larger number cases are needed to confirm.