The benefits of exercise have been recommended in typical and other special populations. However, the evidence for persons with Down syndrome (DS) is still limited. This study was aimed at investigating the impact of an acute bout of aerobic exercise intervention on motor performance, executive function and intrinsic motivation in adolescents and young adults with DS. Ten participants with DS were assigned to an exercise group, who walked on a incremental treadmill protocol for 20 minutes. The exercise intensity was achieved at 66% of their predicted maximum heart rate. Another ten participants with DS were assigned to an attentional control group, who watched a video for 20 minutes. Measures of fine manual dexterity (e.g., Purdue Pegboard test), manual force production (e.g., grip strength test), processing speed (e.g., visual choice reaction time test), verbal processing (e.g., verbal fluency test), attention shifting ability (e.g., The Dimensional Card sorting test), and inhibitory control (e.g., Knock and Tap test) were tested pre and post intervention. An intrinsic motivation scale (e.g., enjoyment and effort) was conducted after the intervention. First, results showed participants significantly improved their performance in manual force production and Knock and Tap Test after the exercise intervention. While it has been proposed that exercise increases arousal status, neurotransmitters, or cerebral vasculature, the exact mechanisms in persons with DS are still unknown. However, our results showed that after treadmill walking, motor and cognitive improvements can be found in individuals with DS, even in a single exercise session. In addition, participants reported higher scores in enjoyment after video viewing than exercise, which may a result from musical effect or too much emphasis on external rewards in their early participation in exercise. These may imply that participants had low intrinsic motivation to an active lifestyle. Further, scores in effort were significantly higher after exercise than video viewing, which indicated their capabilities to perceive their physical exertion. However, other motivational regulations (e.g., introjected and identified regulations) have shown the relationship with exercise behavior in this population. Thus, further study should consider divergent motivational factors in order to implement an effective exercise program.