Stigmatization often puts at risk the health and well-being of children from marginalized groups. One potential protective factor for such children is resilience—one’s capability to adapt flexibly, persistently, and resourcefully to stressful situations. In this study, we investigated the associations among stigmatization, resilience, and hypothalamic-pituitary-adrenal (HPA) axis function in a sample of 645 youths affected by parents infected with HIV. Perceived stigmatization was associated with lower cortisol levels at awakening and flatter cortisol slopes, whereas resilience was independently associated with higher levels of salivary cortisol at awakening and steeper cortisol slopes. We found evidence for an indirect effect of resilience on diurnal cortisol through lower perceived stigmatization. These associations remained significant after we controlled for demographic and health factors and stressful life events. Our findings demonstrate that perceived stigmatization and resilience are associated with HPA-axis functioning in childhood. Broadly, the data suggest that resilience-promoting and stigma-reducing efforts should be considered to improve the health of children from disadvantaged groups.