This study examined the effect of an educational hybrid physical education (PE) intervention on cognitive performance and academic achievement in adolescents. A 9-month group-randomized controlled trial was conducted in 150 participants (age: 14.63 ± 1.38) allocated into control group (CG, n = 37) and experimental group (EG, n = 113). Inhibition, verbal fluency, planning and academic achievement were assessed. Significant differences were observed in the post-test for cognitive inhibition, verbal fluency in animals, and the average from verbal fluency in favour of the EG. With regard to the intervention, verbal fluency in animals, verbal fluency in vegetables, the average of verbal fluency, cognitive inhibition, language, the average of all subjects, the average of all subjects except PE, and the average from the core subjects) increased significantly in the EG. The last five variables (the academic ones and cognitive inhibition) also increased in the CG, in addition to mathematics. This study contributes to the knowledge by suggesting that both methodologies produced improvements in the measured variables, but the use of a hybrid program based on TPSR and gamification strategies produce improvements in cognitive performance, specifically through the cognitive inhibition and verbal fluency.