Background: This study assessed associations between selective school-level factors and students' consumption of fruits and vegetables at school. Better understanding of school factors associated with increased produce consumption is especially important, as students are served more produce items at school. Methods: This cross-sectional study included 5439 seventh- and ninth-grade students from 31 schools in California in 2010. Multilevel regression models estimated whether the odds of consuming fruits or vegetables at school among students eating the school lunch were associated with the length of the lunch period, quality/variety of produce options, or other factors. Results: A longer lunch period was associated with increased odds of a student eating fruits (odds ratio [OR]?=?1.40) and vegetables (OR?=?1.54) at school. Better fruit quality increased the odds of a student consuming fruit (OR?=?1.44). Including a salad bar and involving students in food service decisions increased a student's odds of consuming vegetables (OR?=?1.48 and OR?=?1.34, respectively). Conclusions: This study suggests that institutional factors in schools are positively associated with middle and high school students' consumption of produce items at school. Additional efforts to structure school meal environments to enhance students' consumption of produce items can benefit students' nutrition and health.