The coronavirus disease 2019 (COVID-19) pandemic substantially altered the epidemiology of seasonal influenza and markedly reduced the utilization of anti-influenza agents. Although influenza activity resumed following the relaxation of public health interventions, it remains unclear whether the utilization patterns of anti-influenza agents returned to the pre-pandemic state or changed after the pandemic. Prescription volumes of anti-influenza agents were extracted from the National Database of Health Insurance Claims and Specific Health Checkups Open Data (NDB Open Data) for fiscal years (FY) 2019–2024. Oseltamivir, baloxavir, zanamivir, and laninamivir were evaluated. To compare temporal changes among antiviral agents, prescription volumes were normalized using FY2019 as the reference (index = 100). Utilization of all evaluated anti-influenza agents declined markedly during FY2020 and FY2021. However, the recovery patterns differed substantially among antiviral agents following the resumption of influenza activity. In FY2024, the prescription index reached 297.0 for baloxavir 20-mg tablets and 191.6 for oseltamivir capsules/tablets, whereas zanamivir remained at 57.2. Laninamivir recovered to nearly the pre-pandemic level. These findings indicate that post-pandemic drug utilization differed substantially among antiviral agents. In conclusion, utilization patterns of anti-influenza agents in Japan changed following the COVID-19 pandemic. The heterogeneous recovery observed among antiviral agents suggests that post-pandemic utilization patterns may have been influenced by drug-specific characteristics in addition to the resurgence of influenza activity.