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Purpose: While exercise was found to affect cognitive performance in adolescents, the underlying mechanisms need to be considered. This study compared the effect of a 20 min game-based exercise with different intensities on hormonal responses and potential links to cognitive performance. Methods: 37 adolescents (24 girls and 13 boys; 15–16 years of age) were randomly assigned into light intensity (LIG; 58.64% HRmax), vigorous intensity (VIG; 89.51% HRmax), and control group (CON). The concentration of salivary Testosterone and Cortisol was measured before, immediately after, 20 min and 60 min after the intervention. Results: Repeated-measure ANOVA revealed that neither light nor vigorous game-based exercise acutely affects Testosterone, while Cortisol was higher in the VIG, 20 min after the intervention compared to the LIG and CON. Furthermore, changes in Testosterone were negatively associated with changes in cognitive performance after the acute vigorous intensity exercise (r = −0.63, p = .039) and control condition (r = −0.78, p = .003), but positively associated with post-intervention cognitive performance after the acute light intensity exercise (r = 0.67, p = .012). Conclusion: The intensity of game-based exercise affected Cortisol concentration in adolescents, while Testosterone concentration did not change after the intervention. On the other hand, exercise intensity plays an important role in the association between Testosterone concentration and cognitive performance.