Aerobic exercise has been reported to improve cognitive function in children. Among such functions, the extent to which aerobic exercise affects executive functions, such as working memory and inhibitory control, which are deeply related to academic performance, is an important topic in childcare and education. However, most of the existing research has focused on typical aerobic exercises like jogging. As it is difficult to encourage children to participate in monotonous exercises like jogging for a prolonged period, this poses a barrier to application of research findings in childcare and educational settings. Here, we focused on trampoline exercise, which is more enjoyable for children than typical aerobic exercise, and examined its impact on executive functions. The experiment was conducted using a crossover design with 25 healthy kindergarten children aged 3 to 6 years. Cognitive (1-Back, Go/No-Go, Flanker and Simple reaction time task) and saliva collection were conducted before and after the intervention. In the trampoline condition, participants engaged in 10 minutes of trampoline exercise in the playground, while in the waiting condition, they played freely in the playroom. The results showed significant increases in both cortisol and immunoglobulin A levels only in the trampoline condition. In terms of cognitive parameters, significant changes were observed only under the trampoline condition. These included a significant reduction in the inverse efficiency score of the 1-Back task (p = 0.044), which reflects reaction time adjusted for accuracy, an improvement in the accuracy of the Go/No-Go task (p = 0.023), and a reduced reaction time in the simple reaction time task (p = 0.019). In contrast, no such improvements were observed in the waiting condition (p > 0.05). These findings suggest that short-duration trampoline exercise, which is enjoyable for children, can improve executive function. On the other hand, when comparing changes in these cognitive measures from pre- to post-intervention between conditions, no parameter showed significant differences between the 2 conditions. Therefore, it should be noted that the effects of trampoline exercise on cognitive function cannot be interpreted as being significantly greater than those under the waiting condition. Further validation from a wide range of perspectives is required to develop methods for long-term intervention using trampoline exercise that are beneficial to childcare and early childhood education.