Children who experience early adversity are at increased risk for developing psychopathology, and dysfunction of the hypothalamic pituitary adrenal (HPA) axis is a possible mechanism conferring this risk. This study sought to characterize the association between morning cortisol during different developmental periods and deficits in children's emotion regulation, a core feature of many psychological disorders. Morning cortisol was collected at two time points (i.e., during infancy, M = 13.0 months old, and during early childhood, M = 36.8 months old) from 120 children with histories of child protective services (CPS) involvement. Children completed a lab visit during early childhood (M = 38.6 months old) that involved an observational measure of anger regulation. Results showed that low morning cortisol during infancy, but not early childhood, predicted increased anger dysregulation during early childhood. These results highlight the importance of developmental timing in assessing the effects of HPA axis functioning and suggest that low cortisol during infancy is a risk factor for later emotion regulation difficulties. In this study, we tested the association between morning cortisol during different developmental periods (i.e., infancy and early childhood) and emotion regulation in early childhood among children with a history of early adversity. Low morning cortisol during infancy, but not early childhood, predicted increased anger dysregulation during early childhood. These findings suggest that low morning cortisol during infancy is a risk factor for later emotion dysregulation and highlight the importance of developmental timing in assessing the impact of cortisol regulation.