This study examined whether periods of secure confinement in juvenile detention, jails, and prisons are associated with short- and longer-term increases in adolescent males’ internalizing problems during adolescence and young adulthood. Data came from a longitudinal community sample of 506 male adolescents who were assessed every six months for three years and annually for ten subsequent years. At each assessment, participants reported on their confinement experiences and internalizing problems (i.e., anxiety, depression) during the recall period. Fixed-effects models examined within-individual changes in internalizing problems before, during, and after youth reported any overnight stay in a correctional facility, after controlling for the time-varying confounds of externalizing problem behaviors and previous justice system contact. Additionally, this study tested whether changes in the participants’ internalizing problems varied depending on the confinement facility (i.e., juvenile detention, jail, prison). Overall, results indicated that internalizing problems increased during periods where participants had been confined in a facility. In contrast, there were no changes in internalizing problems in the period prior to confinement and internalizing problems returned to baseline levels in the year following confinement. Facility-specific analyses indicated confinement in prison was associated with the largest increase in internalizing problems. Findings from this study indicate confinement does influence internalizing problems and interventions sensitive to internalizing problems should focus on providing services during confinement and immediate reentry period.