Assessment and monitoring of safety in special education schools is imperative to establish and maintain a safe environment in which students can develop academic and social-emotional skills. The present study describes the development of a student self-report measure, the Safe at School questionnaire. Factorial validity, reliability and concurrent validity was examined in a construction sample of 280 students (68.6% male, age M = 13.29, SD = 2.52) and a validation sample of 1572 students (77.4% male; age M = 14.33, SD = 2.04), representing 233 classes from 20 schools for special education in the Netherlands. Multilevel confirmatory factor analysis was used to examine the factor structure of the Safe at School questionnaire. A model with three correlating factors at the within- and between-group level (Rules and Social Norms, Perceived Own Safety and Perceived Safety of Other Students) showed a satisfactory fit to the data. Reliabilities of the scales were good. Also, measurement invariance for gender was demonstrated, indicating no differences in latent means between boys and girls. Implications for practice and future research are discussed.