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In the past few years, the level of physical fitness in children has decreased globally. According to the SIMCE test carried out in 2015, 45% of 8th year students in Chile were overweight. Moreover, international studies have shown that being overweight is associated with the development of chronic illnesses, negatively affecting cognitive mechanisms and processes. Nevertheless, there is little to no evidence that analyzes the relationship between physical fitness and executive functions in students, at a national level. The aim was to analyze the relationship between cardiorespiratory, musculoskeletal, and motor fitness, and performance in an executive functions test, in students from a public school in the south of Chile. A qualitative, descriptive –correlational, non-experimental, and cross-sectional approach was used. In total, 100 students between 9 and 12 and 11 months of age from a public school in the south of Chile completed the physical fitness assessments through the ALPHA fitness test, and 81 students completed the executive function assessments through the ENFEN test. It was evidenced that students who achieved a longer duration of time and a later stage in the Course Navette test, more centimeters in the standing broad jump (SBJ) test, and a shorter duration in the 4 × 10 shuttle run obtained a better score in the gray trail test. Additionally, students who presented a stronger dominant handgrip scored higher in the colored trail tests. We conclude that students who show a higher level of physical fitness also present a better development of executive functions such as working memory and inhibitory control. In addition, these results suggest physical condition is a factor to consider for better cognitive and school performance.