Developing effective physical fitness exercise program for students is a strategy for improving student’s Academic achievement. The purpose of this study was to investigate the effect of 12 weeks’ health related physical fitness exercise training on student’s Academic achievement. The study employed Experimental research design. From grade 10 male 200 total population, 36 sample students were selected with the age of (experimental group=16.4±6.255, control group = 17.611±1.144) and divided randomly into 2 equal groups. Both the experimental group (number = 18) and control group (number = 18) participated in the typical one classes of 40-minute Physical education per week, but only Experimental group were participated in additional 3 sessions per week of 50 minutes per session of fitness training. Pre and post test results of the selected fitness variables were taken from both groups. Cardio respirator fitness was measured using 12 minute run test, variables were tested by, Muscular endurance were tested using pushups and Muscular strength were measured by using Wall-sit test. The data collected from the study subject was analyzed by using SPSS version 21 software. By using paired t-test the mean differences/changes from pre to post test results of the variables and students average score changes from first to second semester were checked. The results showed health related physical fitness components such as CVE (MD=1860.89), ME (MD=9.33) and MS (MD=25.278), were improved significantly following the 12-week fitness Exercise in EG at (p<0.05). Besides, were significantly reduced, since (p<0.05). Since (p>0.05) However, health related physical fitness components of the Control group have no significant effect on student’s Academic achievement in all selected fitness variables. Therefore, the null hypotheses were rejected in case of cardiovascular accepted in case of muscular strength and muscular endurance. Finally, the researcher concluded that most health related physical fitness components have a significant effect on students’ academic achievement following the twelve-week health related physical fitness exercises &recommended that regular fitness exercises had positive effects on students’ academic ,therefore PE teachers are expected to conduct, implement & encourages fitness