Background <p>This study investigated active Epstein-Barr virus (EBV) infection in children and examined the associations among EBV deoxyribonucleic acid (DNA) load, infection types, disease severity, and immune characteristics.</p> Methods <p>A total of 35,956 pediatric patients who underwent EBV DNA load testing were included. Patients were categorized based on their EBV DNA levels and infection status.</p> Results <p>Spearman’s rank correlation analysis revealed a positive association between EBV DNA levels and the mortality rate, as well as the incidence rates of acute kidney injury (AKI), respiratory failure, cardiovascular complications, coagulation abnormalities, and liver injury. Mortality risk significantly increased when EBV DNA exceeded 1 × 10⁵ copies/mL (adjusted odds ratio: 10.53, 95% confidence interval: 2.38–46.59, <i>P</i> &lt; 0.05). As EBV DNA levels increase, the rise in mortality rate during activation- immunoglobulin G (IgG⁺) was more pronounced than that observed during primary infections. Gaussian mixture model clustering identified two immune clusters. Cluster 0 exhibited elevated pro-inflammatory indicators (IFN-γ, IL-6) and anti-inflammatory indicator (IL-10) levels, along with reduced immune cell counts. This cluster showed higher activation-IgG⁺ and mortality rates compared with Cluster 1.</p> Conclusions <p>An elevated EBV DNA load (&gt; 1 × 10⁵ copies/mL) in children is associated with increased mortality risk. High pro-inflammatory and anti-inflammatory states, coupled with low immune cell numbers, indicate critical condition. Simultaneous examinations of EBV DNA, antibodies, and immune status are recommended, especially for children with EBV DNA &gt; 1 × 10⁵ copies/mL, emphasizing the need for caution in those with activation-IgG⁺ and immune dysregulation.</p>