Few studies have examined how school characteristics are associated with obesity. The purpose of this study was to examine the student- and school-level characteristics associated with being overweight and obese among 12,049 students in grades 9 and 10 (junior students) attending 76 secondary schools in Ontario, Canada. The sample was 49.2% female and the average age was 14.7 years. Overall, 15.0% of the sample was considered overweight and 6.3% of the sample was considered obese. Multi-level regression analysis revealed significant between-school random variation for the likelihood of a junior student (grade 9 or 10) being overweight or obese. For each 1% increase in the prevalence of obese senior students (grade 11 and 12) at a school, the odds of a junior student at that school being overweight or obese increased significantly. Important student-level characteristics included physical activity, screen time sedentary behaviour (e.g., watching television), participation in varsity sports and gender. Future research should evaluate if the optimal population level impact for school-based obesity prevention programming might be achieved by targeting the schools that are putting students at the greatest risk.