Research has identified that perceived weight status is a better predictor of weight control behavior than actual weight status. The purpose of this study was to examine whether the accuracy of weight status perception varies across schools, and to identify the student-level characteristics associated with inaccurate weight status perception among 25,060 grade 9 to 12 students attending 76 schools in Ontario, Canada. Although the majority of adolescents (60.4%) had accurate weight status perceptions, multi-level logistic regression analyses revealed significant between-school variability in the accuracy of weight status perceptions for both males and females. School location and school-level socioeconomic status were the school-level variables analyzed. We identified that males attending urban or suburban schools were more likely to overestimate their weight status compared with males attending rural schools. Important student-level characteristics included grade, weight status, sports participation and social influences. Additional research is required to better understand both the school- and student-level characteristics associated with the accuracy of weight status perceptions among adolescents.