Individual differences in behavioral regulation system (BRS) and stress response system (SRS) functioning may reflect greater biological sensitivity to context. The current study tested whether children's cortisol, a measure of the SRS, was related to observed dysregulated behavior, an indicator of the BRS, in a sample of children admitted for acute psychiatric inpatient care. In addition, cortisol and dysregulated behavior were tested as unique predictors of length of hospitalization over and above demographic factors, prior treatment history, and caretaker-reported psychiatric symptoms. The latter variables were tested as potential moderators of the relations of BRS and SRS functioning to length of hospitalization. Plasma cortisol was collected on the morning following hospital admission for 544 children (ages 6-12; 73% boys; 61% ethnic minority). Dysregulated behavior was operationalized as the mean number of timeouts administered by staff for noncompliant behavior per day of hospitalization. Caretakers reported on youth internalizing and externalizing symptomatology. Higher cortisol was modestly associated with greater dysregulated behavior. In a model including both cortisol and dysregulated behavior, each predicted longer hospitalization. Cortisol was positively related to length of stay only for children previously hospitalized, and the relation of dysregulated behavior to length of stay was stronger for older children. Dysregulated behavior and cortisol are related but independent predictors of acute psychiatric hospitalization duration. Direct measures of the SRS can add to the clinical picture regarding hospitalization in ways that observed behavior and caretaker report alone cannot.