Previous research has studied the influence of physical fitness on academic achievement through executive functions. However, the nature of this relationship remains unclear. This study aimed to analyze how cardiorespiratory fitness (CRF) and executive functions are associated with academic achievement and to examine whether the relationship between CRF and academic achievement is mediated by executive functions in schoolchildren. Methods This was a cross-sectional study including 570 schoolchildren, aged 8 to 11 years, from Cuenca, Spain. Data were collected from September to October 2017. Sociodemographic variables, family socioeconomic status, pubertal status, academic achievement, CRF (20meter shuttle run test) and executive functions (inhibition, cognitive flexibility and working memory, NIH Toolbox battery in Spanish, v 1.8; iPad Pro, Apple, Inc.) were measured. Results Overall, ANCOVA models controlling for age, gender and mother educational level showed higher scores in language and mathematics in children in higher categories of CRF, inhibition, cognitive flexibility and working memory than in children in lower categories. The effect sizes were moderate (p < 0.05, partial eta squared: from 0.05 to 0.12). Moreover, the mediation analysis showed that inhibition partially mediated the relationship between CRF and language (c' = 0.058; IC = [0.005; 0.028]) and mathematics (c' = 0.064; IC = [0.005; 0.030]) grades. Similarly, cognitive flexibility mediated CRF's relationship with language (c' = 0.059;