Many adolescents in the juvenile justice system have been exposed to trauma, which has been linked with negative outcomes that may lead to ineffective adjustment while incarcerated. Trauma may decrease a youth’s feelings of fairness and safety, which may increase misconduct. The present study examined the relationship between post-traumatic stress disorder (PTSD) symptoms, perceptions of fairness and safety, and rates of institutional misconduct in a subsample of youth (n = 386) who participated in the Pathways to Desistance study. A serial multiple mediation model found that PTSD symptoms were not significantly associated with perceptions of fairness, safety, or institutional misconduct. Relationships were found between perceptions of fairness and safety, and between perceptions of safety and institutional misconduct. Results also indicated differences in perceptions of fairness and safety based on gender, age, and ethnicity. Perceptions of fairness and safety may be an avenue for intervention to improve adjustment within the juvenile justice system.