This study examined outcomes for 320 youth in a Center for Mental Health Services system-of-care demonstration site. Youth received wraparound-only (n = 213), MST-only (n = 54), or wraparound + MST (n = 53). Participants were 12 years old on average and mostly White (90%), and 75% were Medicaid-eligible. Service use and functional and clinical outcomes were examined at 6-month intervals out to 18 months. All three groups improved over the study period. The MST-only group demonstrated more clinical improvement than the other groups. Functional outcomes did not differ significantly across groups. Youth in wrap + MST had higher baseline severity and experienced less clinical and functional change than the other two groups, despite more mental health service use. Targeted, evidence-based treatment may be more effective than system-level intervention alone for improving clinical symptoms among youth with serious emotional disorders served in community-based settings. New or amended approaches may be needed for youth with the most severe disorders.