The COVID-19 pandemic has affected the globe since the late 2019 and caused immense infections and deaths worldwide, thereby posing severe challenges to medical institutions. Regarding patient treatments, a common secondary infection following influenza is associated with symptoms induced by gram-positive bacteria such as streptococcus pneumoniae. A review of relevant literature suggests that the during the COVID-19 pandemic, numerous patients have received empiric antimicrobial therapy. However, the incident rates of secondary diseases or coinfection during the COVID-19 pandemic are not higher than those during influenza epidemics. Consequently, an immediate problem emerges regarding the increased use of empiric antibiotics during the current pandemic, which may lead to the increase of multiple drug resistant organisms. A structural problem underlying this situation is incurred by difficulty associated with the operation of the antimicrobial stewardship program (AMS) in hospitals. For example, AMS personnel have been reassigned to pandemic prevention units, preventing them from maintaining communications with multiple teams. In addition, the pandemic has impeded the basic monitoring of nosocomial infections or multiple drug resistant organisms. Therefore, approaches to addressing the effect of the COVID-19 pandemic on antimicrobial stewardship and preparing for emerging pandemics in the future are critical topics that merit further exploration.