Nonpharmaceutical interventions (NPIs) to control COVID-19 have decreased the incidence of many pediatric infectious diseases. The epidemiology of βand γherpesvirus infections might have been affected by NPIs. The aim of this study was to elucidate changes in trends in βand γ-herpesvirus infections and complex febrile seizures (cFS) of viral etiology before and during the COVID-19 pandemic. Between April 2017 and March 2021, febrile children aged ≤5 years were enrolled. Detection of EBV, CMV, HHV-6B, and HHV-7 DNA in serum was performed using real-time PCR. The epidemiology of viral infections and cFS were compared between the prepandemic and pandemic periods. During the observation period, 1432 serum samples were collected. The mean number of febrile children decreased during the pandemic period, but the number of patients with HHV-6B infection increased from 35 (9.3% of all febrile children) per year before the pandemic to 43 (15.5%) during the pandemic. The change in the proportion of patients with primary HHV-6Binfection was 6.50% (95% confidence interval [CI], 2.05%-11.3%; p = 0.0047). The mean number of patients with cFS decreased during the pandemic period, but the number of patients with HHV-6B-associated cFS was stable throughout the observation period. Therefore, the change in proportion of patients with cFS caused by primary HHV-6B infection was 49.5% (95% CI, 12.2%-60.5%; p = 0.0048). The disease burden of primary HHV-6B infection among patients in the emergency room remained unchanged, with a significant increase in the relative proportion after the COVID-19 pandemic began.