Background: Socioeconomic status (SES) influences students' school perceptions and affects their performance, engagement, and personal beliefs. This study examined the effects of school population SES and school resources on the association between student SES and student perceptions. Methods: School liking, classmate social relationships, family affluence, and experience of hunger were assessed in a nationally representative sample of 12,642 students (grades 5-10) in the 2009-2010 Health Behavior in School-Aged Children study. School characteristics included school meal program, Title 1 dollars received per student, school resources, and urban/rural status. Multilevel analysis was used. Results: At the individual level, both school liking and social relationships were negatively associated with student grade level. Boys liked school less and had more positive perceptions of social relationships than girls. Students in rural schools and who experienced hunger liked schools less and had poorer perceptions of social relationships than their respective counterparts. School-level percentage of students eligible for free/reduced meals accounted for 33% of the between-school variance in social relationships. Conclusions: Family and school economic characteristics and grade level influenced students' school perceptions. The associations between student SES, school population SES, and school perceptions suggests that school health professionals should recognize and address student economic issues at school.