The current scientific literature has shown significant disparity in results when physical activity is linked to academic achievement among adolescents. Thus, the main objectives of this study were (1) to analyze the relationship among students’ academic achievement, intention to be physically active, and physical activity levels depending on the country (Spain or Chile), as well as to analyze these relationships based on students’ socio-economic status, type of school, school year, gender, and body mass index; and (2) to analyze the differences between all these variables depending on the students’ country and gender. In total, 3052 adolescents participated in the research (14.58 ± 1.39 years): 734 Chilean students (336 males and 398 females) and 2318 Spanish students (1180 males and 1138 females). Various questionnaires were used to measure the study variables. The results revealed significant relationships between academic achievement and the rest of the variables in Spanish adolescents, but in the Chilean population, academic achievement was significantly related only to socio-economic status and the type of school. Moreover, Spanish students obtained higher scores, especially the males, except for academic achievement, which was higher in females. There were also significant differences in academic achievement, intention to be physically active, physical activity levels, and socio-economic status depending on the country, with all scores being higher in Spain. Given the results, the country seems to be an important factor when comparing academic achievement and physical activity levels, besides other demographic variables.