Background: Students with special educational needs and disabilities (SEND) are more likely to exhibit behaviour difficulties than their typically developing peers. Aim: The aim of this study was to identify specific risk factors that influence variability in behaviour difficulties among individuals with SEND. Sample: The study sample comprised 4,228 students with SEND, aged 5-15, drawn from 305 primary and secondary schools across England. Method: Explanatory variables were measured at the individual and school levels at baseline, along with a teacher-reported measure of behaviour difficulties (assessed at baseline and at 18-month follow-up). Results: Hierarchical linear modelling of data revealed that differences between schools accounted for between 13% (secondary) and 15.4% (primary) of the total variance in the development of students' behaviour difficulties, with the remainder attributable to individual differences. Statistically significant risk markers for these problems across both phases of education were being male, eligibility for free school meals, being identified as a bully, and lower academic achievement. Additional risk markers specific to each phase of education at the individual and school levels are also acknowledged. Conclusion: Behaviour difficulties are affected by risks across multiple ecological levels. Addressing any one of these potential influences is therefore likely to contribute to the reduction in the problems displayed.