The study aimed to elucidate the influence of cognitive engagement comprised in an acute bout of exergame-based physical activity on executive functions (inhibition, cognitive flexibility) in adolescents. Therefore, the level of cognitive engagement and the intensity of physical activity were systematically varied across three experimental conditions. Sixty-five healthy male adolescents (13-16 years) were randomly assigned to one of three conditions: (a) physical activity with high levels of cognitive engagement during active video gaming, (b) physical activity with low levels of cognitive engagement during active video gaming, (c) sedentary with low levels of cognitive engagement during passive video watching. Manipulation checks, including subjective and objective operationalizations of cognitive engagement, were applied. Executive functions were assessed before and after each condition using the D-KEFS design fluency test. Results showed that cognitive engagement, operationalized by subjects' ratings and heart rate variability, differed between conditions. The physical activity condition with a high level of cognitive engagement resulted in significantly better performance in cognitive flexibility compared to conditions with low levels of cognitive engagement. Regarding benefits for executive functions in male adolescents, the results indicate that acute physical activity with high cognitive engagement could be more efficient than physical activity of the same intensity with low cognitive engagement. Even though further evidence is needed, these results extend previous research and suggest a methodological approach for measuring cognitive engagement.