The COVID-19 outbreak affected the daily lives of individuals with Down syndrome, who were considered to have a higher risk of severe infection. While several studies have reported mental health issues in children and/or parents in the general population, no study has focused on people with Down syndrome and their caregivers. This study investigated the disinfection behaviors of individuals with Down syndrome and their caregivers' stress. A cross-sectional retrospective survey was conducted in October 2020. Caregivers of children and adults with Down syndrome were administered questionnaires including measures for practiced disinfection behavior in children, caregiver's child-related stress, and psychological distress. About half of the respondents' children practiced hand hygiene and mask-wearing behaviors, while physical distancing was performed less frequently. Habitual practices in physical distancing are affected by intellectual function. Logistic regression showed that caregivers' stress was associated with the irritability of individuals with the disorder (adjusted odds ratio [OR] = 8.44, 95% confidence interval [CI] 1.69-42.09) and the burden of infection-prevention behaviors for people with Down syndrome (adjusted OR = 4.26, 95% CI 1.88-9.65). This study showed the characteristics of disinfection behaviors in individuals with Down syndrome and associated factors for serious caregiver stress.