To reduce childhood obesity and improve student health, in 2009, the Georgia General Assembly passed the School Health and Physical Education (SHAPE) Act. This act requires schools to conduct an annual fitness assessment for students enrolled in a physical education (PE) course taught by a certified PE teacher. However, in Georgia there is no requirement that middle school students take PE. This policy makes Georgia’s middle school level unique since PE is required for elementary students annually and for high school students as a one-unit health and physical education graduation requirement. In Georgia, males have historically outperformed females on the FitnessGram© tests used for the annual fitness assessment, and males participate in PE at higher rates. This study utilized physical fitness, school characteristics, and PE participation data to study the association of school characteristics with PE participation and body mass index (BMI) and aerobic capacity fitness outcomes. Data for 315 middle schools, from the 2012 through 2017 school years, were merged and analyzed using descriptive statistics and multiple linear regression models in a cross-sectional study. An increase in the number of students receiving free or reduced lunch was associated with a decrease in PE participation for both males and females (-.014, p<.01) and a decrease in HFZ BMI achievement and HFZ aerobic capacity achievement for all students (-.014 and -.039, respectively, p<.01). Furthermore, an increase in male PE participation was associated with increased HFZ aerobic capacity achievement for males only (.049, p<.01). Results showed an association between school socioeconomic status indicators and PE participation rates, and fitness outcomes. Associations with PE participation and HFZ achievement were also found for certain school-level variables, including number of full-time teachers, pupil-teacher ratio, and city and town school locations, compared to rural school location. Interventions to decrease health disparities as well as to remove barriers to PE participation and effective PE programming are needed at middle schools serving socioeconomically disadvantaged youth. In addition, middle schools should implement interventions to improve fitness outcomes for female students. Increasing resources at marginalized schools may also decrease health disparities.