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Background There is an increasing prevalence of physical inactivity during childhood, which is associated with a variety of health problems. However, the mechanisms by which acute exercise benefits cognition in childhood remains unknown. Here we describe the protocol for a randomized crossover trial called SNEACY (Sympathetic Nervous System & Exercise Affects Cognition in Youth), a study designed to better understand mechanisms linking acute exercise and cognition in 9–10-year-old healthy, cognitively normal children. Methods Children from the Greater Boston, MA region will be recruited to participate in this single center study. A randomized crossover design will be utilized, such that participants will act as their own controls, through initial randomization to condition assignment and condition counterbalancing across participants. One hundred three children will participate in three randomized acute interventions: moderate intensity treadmill exercise (20 min, 70–75% of their maximal heart rate), seated rest (20 min), and a Trier Social Stress Test for Children (14 min). These visits will occur on 3 three separate days, approximately 5–8 days apart. Before and after each intervention, children complete a variety of cognitive tasks measuring attentional inhibition while their neuroelectric activity is recorded. Variables of interest include EEG data, accuracy and reaction time, academic achievement, and salivary alpha amylase. Academic achievement is also assessed following interventions. In addition, children provide passive drool samples throughout the interventions to measure various biomarkers that may explain the acute exercise benefit on cognition. Discussion The results from this study could influence educational and public health recommendations to enhance cognition and learning in pre-adolescent children. Trial registration ClinicalTrials.gov NCT03592238. Registered on 19 July 2018