Atopic dermatitis (AD) is a chronic inflammatory skin disease that is common in children and is increasing worldwide. This study aimed to identify differences in children’s health behavior and social-emotional health status based on AD diagnosis at late school age. For this purpose, we conducted a descriptive survey using the 12th Panel Study on Korean Children data obtained in 2019. The data were analyzed using descriptive statistics, the Rao–Scott χ2 test, and a t-test using a complex sample analysis. A total of 1412 11-year-old Korean children participated in the study, of whom an estimated 8.2% were diagnosed with AD. In the children diagnosed with AD, the transition from exclusive breastfeeding to mixed feeding was later than that in children without AD (F = 5.71, p = 0.024), and the prevalence of AD in their parents was higher (F = 6.97, p = 0.014). Regarding health behaviors, the children diagnosed with AD had a higher intake frequency of protein (F = 5.41, p = 0.028) and vegetables (F = 6.09, p = 0.020). Regarding social-emotional health, subjective health status (F = 3.94, p = 0.026) and friend relationships (F = 2.95, p = 0.007) were lower in the children diagnosed with AD. These results, as preliminary data for interventions for school-aged children with AD, suggest that the difficulties of children’s peer relationships should be considered and dealt with in further interventions.