The aim of this cross-sectional study was to investigate the relationship between physical fitness, executive function, and academic performance in children and adolescents. A total of 131 students (49% female) aged 10–15 years from a public school in Rio de Janeiro were assessed in executive functions (hearts and flowers, Corsi’s block, and digit span tasks), academic performance (Portuguese, reading, math, and overall school grade), physical tests (touch test disc, agility, lower limb and upper limb explosive strength), and anthropometric measurements. Regression results showed that the composite of sports-related fitness measures was the best predictor of executive functions (β = 0.472; t = −6.075 p < 0.001). Decision tree classifier analysis showed that the combination of factors that discriminated better and worse executive function groups were better performance in hand–eye coordination (TTD), math, and upper limb strength (ULEST). Sports-related fitness is significantly correlated with executive function. Hand–eye motor coordination has been identified as the most important predictor of improved cognitive outcomes, surpassing even academic skills. These findings should be considered in the design of physical activity programs in school settings, which may have a positive impact on child development, reflected in the reduction of academic and socioeconomic disparities.