This study examines the situation and challenges of after-school daycare centers during Japan’s first state of emergency declared in response to COVID-19. A survey in Tokyo’s Tama area identified issues such as limited rest areas, insufficient space, and staff shortages. Restrictions on adjacent facility use hindered efforts to avoid the “Three Cs.” Staff voiced concerns about overcrowding and limited infection control. To prepare for future emergencies, improving infrastructure and enabling flexible space use are essential. Further research is needed on optimal room sizes and layouts to ensure safe, effective childcare environments.