Developing effective aerobic exercise program for students is a strategy for improving cardio respiratory fitness and body composition. The purpose of this study was to investigate the effect of aerobic exercise on cardio respiratory fitness and body composition variables. The study employed Experimental research design. 30 male students of Gonji preparatory school with the age of (EG=18.93±4.803, CG = 19.8±.94) had divided randomly into 2 equal groups. Both the exercise group (EG, n = 15) and control group (CG, n = 15) participated in the typical 1 classes of 40-minute Physical education per week in schools, but only EG participated in additional 3 sessions per week of 40 to 60 minutes per session of exercise training, which comprised as walking, jogging, running and rope skipping. Both groups had taken pre and post-testing and all the subjects participated in physical fitness tests: cardio respiratory fitness was measured using 12 minute run and three minute step test and Body Composition variables were measured using Bio electrical Impedance Analyzer. The data collected from the study subject was analyzed using SPSS version 16 software by paired t-test with level of significant 0.05. The results showed aerobic Exercise significantly improved cardio respiratory fitness, skeletal muscle percentage and resting metabolism in EG at (p<0.05). Besides, there were significantly reduced body mass index, visceral fat and body fat percentage (p<0.05). In case of body age, no significant change was observed in both groups. Furthermore, no significant differences were found in all of the variables in CG (p>0.05). Based on this finding, it can be concluded that twelve weeks aerobic exercise has positive effect on improvement of cardio respiratory fitness and body composition variables.