There is a growing interest in determining which variables contribute to students’ academic performance, since this performance is associated with their wellbeing and with the progress of the nation. This study analyzed whether different variables (executive functions and physical activity levels, gender and academic year) of 177 Spanish Compulsory Secondary School students contributed to their academic performance. The Behavior Rating Inventory of Executive Function 2 (BRIEF-2), Physical Activity Questionnaire for Adolescents (PAQ-A) and an ad hoc questionnaire were used to determine the students’ executive functioning, physical activity level, gender and academic year, respectively. Students’ grades were considered to be indicators of their academic achievement. Seven multiple linear regression models were constructed using the R computing language to examine the association between academic achievement (considered in each of the 5 subjects: Language, Mathematics, Geography and History, English and Physical Education; the mean of the instrumental subjects—Language and Mathematics—and the mean of all the subjects) and the independent variables. The results indicated that executive functions, physical activity and gender contributed to academic performance, but academic year did not. This suggests that students with good executive functions, who perform physical activity and are female, would have better academic achievement. This information should be considered when designing interventions to improve student academic achievement.