An educational physical education (PE) hybridization program based on the personal and social responsibility model and gamification strategies was used in order to explore the effect on cognitive performance and academic achievement. A 9-month group-randomized controlled trial was conducted, with 150 participants (age: 14.63 ± 1.38) allocated into the 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 (named animals), and the mean of both verbal fluency tasks in favor of the EG. With regard to the intervention, verbal fluency (named animals), verbal fluency (named vegetables), the mean of both verbal fluency tasks, 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. Values for the last five variables (academic variables and cognitive inhibition) in addition to mathematics also increased in the CG. This study contributes to the current knowledge by suggesting that both methodologies produced improvements in the measured variables, but the use of the hybridization resulted in improvements in cognitive performance, specifically with regard to cognitive inhibition and verbal fluency.