A single bout of physical activity can benefit cognitive and brain function; however, the biological mechanisms underlying this acute effect remain unclear. This study investigated changes in salivary alpha-amylase (sAA), a marker of sympathetic nervous system activity, and salivary cortisol (CORT), reflecting hypothalamus-pituitary-adrenal (HPA) axis activity, as candidate mechanisms mediating the effects of acute exercise on brain function and cognition in children. In a pre-post randomized crossover design, 104 children (ages 9-10) completed exercise, the Trier Social Stress Test for Children (TSST-C; active control), and seated rest (passive control) conditions, with neuroelectric activity (P3 amplitude and latency) and attentional inhibition as outcomes. Structural equation modeling was performed to examine sAA and CORT as mediators of the relationship between exercise and neuroelectric and cognitive outcomes. Moderated mediation was used to test if the magnitude of the sAA-mediated path varied as a function of pre-intervention baseline CORT. Exercise led to decreased sAA compared to both controls and lower CORT than TSST-C, controlling for pre-intervention baselines. Post-exercise reductions in sAA mediated reduced variability in attentional inhibition and trended for accuracy. Exercise effects on neuroelectric activity (P3 amplitude) varied with baseline CORT. This study is among the first to investigate the biological underpinnings of acute exercise-induced changes in cognition in children using molecular, behavioral, and brain imaging measures. Findings implicate sAA as a candidate mechanism through which exercise acutely benefits neurocognition, moderated by individual differences in HPA axis activity.