Background: To advance research on youth fitness promotion it is important to understand factors that may explain the disparities in fitness. Methods: We evaluated data from the FitnessGram NFL PLAY60 Partnership Project to examine school factors influencing aerobic capacity (AC) and body mass index (BMI) in schoolchildren. Individual observations for AC (157,971 students from 675 schools) and BMI (178,274 students from 630 schools) were aggregated to compute the percentage of students achieving the Healthy Fitness Zone (HFZ). We examined achievements using adjusted linear regression models with socioeconomic status (SES), minority status, region, enrollment, and grade as factors. Results: The mean HFZ for AC and BMI were 51.6% and 56.9%, respectively. SES, minority status, and enrollment were all significantly associated with AC HFZ among boys, and SES and enrollment were significant predictors of AC HFZ in girls. SES and location were significantly related to BMI HFZ among boys but only SES significantly predicted BMI HFZ in girls. Schools with higher SES had higher AC and BMI HFZ achievements. Conclusions: SES was consistently associated with health-related fitness, independent of sex, but not minority status.