To analyze the effects of an intervention focused on increasing the time and intensity of Physical Education (PE), on adolescents' cognitive performance and academic achievement. A 4-month group-randomized controlled trial was conducted in 67 adolescents from South-East Spain, 2007. Three classes were randomly allocated into control group (CG), experimental group 1 (EG1) and experimental group 2 (EG2). CG received usual PE (two sessions/week), EG1 received four PE sessions/week and EG2 received four PE sessions/week of high intensity. Cognitive performance (non-verbal and verbal ability, abstract reasoning, spatial ability, verbal reasoning and numerical ability) was assessed by the Spanish Overall and Factorial Intelligence Test, and academic achievement by school grades. All the cognitive performance variables, except verbal reasoning, increased more in EG2 than in CG (all P < 0.05). Average school grades (e.g., mathematics) increased more in EG2 than in CG. Overall, EG2 improved more than EG1, without differences between EG1 and CG. Increased PE can benefit cognitive performance and academic achievement. This study contributes to the current knowledge by suggesting that the intensity of PE sessions might play a role in the positive effect of physical activity on cognition and academic success. Future studies involving larger sample sizes should confirm or contrast these preliminary findings.