Abstract: The study was conducted to compare the effects of aerobic and anaerobic workouts on performance enhancement of selected physical fitness variables among first year Sport Science students at Wolaita Sodo University. Thirty (15 male and 15 female) students from Sport Science department were selected as subjects and their age were 19 - 21 years. Subjects were randomly assigned to aerobic training group (5 male, 5 female,) anaerobic training group (5 male, 5 female) and control group(5 male, 5 female). The experimental groups were participated in a supervised aerobic and anaerobic training program 3 days/week for 12 weeks. The control group did not participate in any of the program. The physical fitness variables selected for the study were: cardiovascular endurance, muscular strength, muscular endurance, flexibility, body composition and Agility. Data were analyzed using ANOVA and multiple comparison of post test means were held to discover which treatment means differ at 95% confidence interval by using Fisher LSD. The results obtained in this study indicate that there was significant improvement in selected physical fitness variables due to the effects of aerobic and anaerobic training (p < 0.05) .This study proved that aerobic exercise was significantly better than anaerobic exercise in improving cardiovascular endurance and flexibility(p < 0.05) and anaerobic exercise was significantly better than aerobic exercise in improving muscular endurance, muscular strength and agility(p < 0.05) while both exercises had almost the same effect in improving the body composition of the participants.