Positive perceptions of school climate correlate with many dimensions of academic well-being and student health. Unfortunately, some existing research finds more favorable perceptions in middle school for general education students (GENs) than for students with disabilities (SWDs). Given the importance of ninth grade to student success, it is important to know if perceptions improve when students go to high school, if they improve more for GENs than SWDs, and if they are mediated by school characteristics. Our analysis of rich student-level longitudinal data suggests that students perceive improvements in school climate when they transition to high school, school characteristics do mediate perceptions, and perceptions of GENs improve more (or decline less) than those of SWDs, resulting in gaps favoring GENs.