The study investigated whether school-level protective factors could moderate the effects cumulative risk has upon behavior difficulties in children with special educational needs and disabilities (SEND). The sample comprised 4,288 children identified with SEND: 2,660 pupils within 248 primary schools, and 1,628 pupils within 57 secondary schools. Risk factors associated with increases in behavior difficulties over an 18-month period were summed to a cumulative risk score. Various school-level factors were added to multilevel models, with interaction terms computed between cumulative risk and these variables to assess their potential protective effects. The primary school model revealed a significant interaction between cumulative risk and school academic achievement in predicting behavior difficulties. Higher levels of achievement in primary schools help reduce behavior difficulties for children most at risk. The secondary school model evidenced a significant interaction between cumulative risk and school percentage of students eligible for free school meals (FSM). Lower proportions within a school of children eligible for FSM were associated with reductions in behavior difficulties for children at high levels of risk. Interventions aimed at improving school-level academic achievement and targeting high-risk students attending schools with large proportions of children eligible for FSM would be beneficial.