This study compared cognitively challenging physical activity games and health-related fitness activities in terms of their effects on students’ executive functions and situational interest in physical education. A total of 102 fourth- and fifth-grade students (56 boys, 46 girls) participated in this study. A group-randomized controlled trial design involving an acute experiment was used. Two intact classes of students (one fourth-grade and one fifth-grade) were randomly assigned to each one of the three groups. Students in Group 1 participated in cognitively challenging physical activity games, students in Group 2 participated in activities for developing their health-related fitness, and Group 3 students were the control group without physical education. Executive functions were measured pre- and post-intervention with the design fluency test, whereas situational interest was only measured post-intervention with the situational interest scale. Group 1 students who played cognitively challenging physical activity games had increased their executive functions’ scores more than the Group 2 students involved in health-related fitness activities. Students of both these groups outperformed control group students. Moreover, Group 1 students reported higher levels of instant enjoyment and total interest than Group 2 students. The results of this study suggest that cognitively challenging physical activity games can be an effective means for enhancing executive functions, and motivate students to be involved in interesting and enjoyable forms of physical activity.