The current evidence for a relation between children’s heart rate measures and their academic performance and executive functioning is infancy. Despite several studies observing dose-response effects of physical activity on academic performance and executive function in children, further research using objective measures of the relative intensity of physical activity (e.g., heart rate) is warranted. The present study aimed to inspect associations between heart rate response and various academic performance indicators and executive function domains. A total of 130 schoolchildren between the ages of 9 and 13 years (M = 10.69, SD 0.96 years old; 56.9% boys) participated in a cross-sectional study. Children’s heart rate data were collected through participation in physical education classes using the polar TeamTM hardware and software. One week before heart rate measures, academic performance was obtained from the school records in maths, Spanish language, Catalan language, physical education, and Grade point average. Executive function was measured by two domains, cognitive flexibility with the Trail Making Test and inhibition with the Stroop test. Associations between children’s heart rate data and academic performance and executive function were analyzed using regression models. Academic performance was found to be positively related to four heart rate measures (β range, 0.191 to 0.275; all p < 0.040). Additionally, the hard heart rate intensity level was positively related to two academic indicators (β range, 0.183 to 0.192; all p < 0.044). Three heart rate measures were associated with two cognitive flexibility subdomains (β range, −0.248 to 0.195; all p < 0.043), and three heart rate measures were related to one inhibition subdomain (β range, 0.198 to 0.278; all p < 0.028). The results showed slight associations of heart rate responses during physical education lessons with academic performance but did not clearly indicate associations with executive function. Future experimental studies testing associations between different bouts of intensity levels are needed to disentangle the relationship with brain function during childhood.