Physical activity and cardiorespiratory endurance have both been shown to associate with academic achievement; however, there is a paucity of work examining mediating effects. The purpose of this study was to examine the relationship between cardiorespiratory endurance and mathematics performance using school day physical activity as a mediator. The sample consisted of 174 middle school students (mean age = 13.4 ± 0.5 years) recruited from one middle school located in the US. Cardiorespiratory endurance was assessed using Progressive Aerobic Cardiovascular Endurance Run laps, school day step counts were recorded for 5 days using pedometers, and mathematics performance was assessed using standardized tests. A bootstrapped mediation analysis revealed that school day steps mediated the relationship between PACER laps and math test scores (Average Causal Mediated Effect = 0.05, 95% C.I.: 0.03-0.07, p < 0.001). These effects were independent of age and Body Mass Index. Approximately 81.1% of the total effect between cardiorespiratory endurance and math test scores was mediated through daily step counts with the full model explaining 48.8% of the total variance in math test scores. In a sample of middle schoolers, school day step counts mediated the relationship between cardiorespiratory endurance and mathematics performance, suggesting that providing opportunities for children and adolescents to be active during the day may facilitate learning through behavioral and physiological mechanisms.