The purpose of this study was to define that the effect of aerobic exercise on the expression of BDNF and Cortisol in middle-school Students. The subjects were twenty middle schoolers of 15 years-old age whose cohorts were divided into aerobic exercise group (EG, n=10) and control group (CG, n=10). Frequency of the aerobic exercise was three times a week for 8 weeks. To be equal to the workload of the exercise, the customized aerobic exercise was set up for 200㎉ consumption of each individual by formula. Blood samples data was collected before and after the experiment, the conclusion as follows: 1. The expression of BDNF showed a significant increase of 4244.33pg/㎖ from 23321.67±6247.04pg/㎖ to 27566.00±5647.61pg/㎖ (p<.001), 2. The Cortisol showed a significant decrease of 2.43㎍/dL from 13.62±4.07㎍/dL to 11.19±2.31㎍/dL(p<.05) 3. The expression of BDNF and Cortisol between two cohorts was significant after the aerobic exercise(p<.05). The result of this study explained that aerobic exercise was positive for the expression of BDNF and decrease of Cotisol in the middle-school students.