Promotion of healthy active behaviors should start from early ages, as behaviors learned in youth are more likely to endure. A fundamental body of research in this field focuses on the implementation of programs within physical education (PE), thanks to its favorable characteristics. However, traditional PE based on exercise training and controlling styles seems to have weaker association with students’ health benefits. For this reason, the aim of this study was to assess the effects of a game-based PE program on physical fitness and psychological health in schoolchildren aged 10 to 12 years old. A total of 252 students were distributed in experimental (EG, games-centered activities) and control (CG, traditional exercise training activities) groups. The program lasted 6 months. Health-related physical fitness components, psychological wellbeing, self-esteem, stress, and anxiety were assessed before and after the treatment. Both groups increased physical fitness at post-test; however, cardiorespiratory fitness did not improve. No differences were found between the groups at post-test. Our results show that games may be as effective as traditional training methods; yet, they suggest that PE alone may be insufficient for obtaining substantive benefits in cardiorespiratory fitness, regardless of the type of task presented.