Systems of care can be used to help coordinate and direct resources both external and internal to a school, thereby providing critical supports for students with emotional and behavioral challenges that historically have not been available to educators. In this study, hierarchical linear modeling was used to longitudinally examine school functioning change trajectories for a sample of students who participated in the Dawn Project system of care in Indianapolis, Indiana. The investigation was driven by the hypotheses that improvements in school functioning would be associated with improvements in clinical functioning over time and also that demographic characteristics would not be associated with such changes in school functioning. In general, the findings supported these hypotheses. Specifically, school functioning was found to significantly improve between the time students enrolled in the system of care and up to 36 months postenrollment. Moreover, longitudinal improvements in school functioning were significantly associated with improvements in clinical functioning, even after controlling for the influence of time. Although the relationship between school and clinical functioning is not well understood, these findings suggest that an interdependent relationship exists, highlighting the importance of simultaneously targeting school and social-emotional challenges. (Contains 3 tables.)