The present longitudinal study used a social-ecological framework to explore the extent to which peer victimization and aggression were associated with changes in concentration problems and emotion regulation among elementary students in general versus special education, while accounting for student demographics and school contextual factors. Data come from a multilevel, longitudinal dataset including 7,314 students (kindergarten through Grade 2) across 37 elementary schools. Multilevel analyses indicated that on average, students in special education had worse trajectories, including higher concentration problem scores and lower emotion regulation skills over time than students in general education. Children who were victimized and in special education displayed significantly more concentration problems and worse emotion regulation skills at baseline as compared with other students. The findings highlight the risks associated with prolonged victimization among children in special education. Implications for prevention programming targeting social-emotional functioning and special education populations are discussed.