The purpose of this study was to examine the effects of aerobic, resistance, and combined exercise training on cardiorespiratory and musculoskeletal fitness in postpubertal adolescents with obesity. After a 4-week supervised moderate-intensity exercise run-in, 304 adolescents aged 14–18 years with body mass index ≥85th percentile were randomized to 4 groups for 22 weeks of aerobic training, resistance training, combined training, or a nonexercising control. All participants received dietary counselling with a maximum daily energy deficit of 250 kcal. Cardiorespiratory fitness (peak oxygen consumption) was measured by indirect calorimetry using a graded treadmill exercise test. Musculoskeletal fitness was measured using the 2003 Canadian Physical Activity Fitness and Lifestyle Appraisal tests (hand grip, push-ups, partial curl-ups, sit and reach, and vertical jump). Muscular strength was assessed using an 8-repetition maximum test on the bench press, seated row, and leg press machines. A greater increase in peak oxygen consumption in the aerobic exercise group (30.6 ± 0.6 to 33.4 ± 0.7 mLO2/kg/min) was measured relative to the control group (30.6 ± 0.5 to 30.9 ± 0.7 mLO2/kg/min) (p = 0.002). Similarly, the number of partial curl-ups increased in the aerobic group (19 ± 1 to 23 ± 1) while no differences were measured in the control group (19 ± 1 to 20 ± 1) (p = 0.015). Increases in muscular strength and number of push-ups were greatest in the resistance group versus the control and combined groups versus the aerobic group (p < 0.05). In conclusion, aerobic training had the strongest effect on cardiorespiratory fitness, while resistance and combined training improved both muscular strength and endurance more than control and aerobic training alone, respectively, in adolescents with obesity.