In the aftermath of several school shooting incidents in recent years, students’ perceptions of unsafe schools has been a major concern for parents, teachers, school officials, school practitioners, and policy-makers. Using Bronfenbrenner’s ecological systems framework, we examined the micro-, meso-, and exosystem level factors associated with perceptions of unsafe school environments in a nationally representative sample of 10- to 15-year-old youth in the United States. We found that for the socio-demographic characteristics, students who were older, male, and poor had increased risks of perceiving higher levels of unsafe school environments. Within the microsystem of the family, our results indicate that parent-youth discussions of school activities/events decreased the risk of students perceiving unsafe schools. All of the school environment variables—ease of making friends, teachers’ involvement, observed weapon carrying, and school rule enforcement—were related in the expected direction to students’ perceiving their schools as unsafe. At the mesosystem level, findings from our study demonstrate that variables measuring parental school involvement were unrelated to perceptions of school safety. Finally, at the exosystem level, we found that students’ perceptions of residing in a safer neighborhood and residence in a non-central city metropolitan area, compared with a central city, decreased the odds of perceiving school environments as unsafe. School policy and practice implications are discussed.