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Whilst participation in regular exercise and sport has generally increased over recent decades globally, fundamental questions remain regarding the influence of growth, maturation, and sex on the magnitude of training response throughout adolescence. Trained (108 participants, 43 girls; age: 14.3 ± 1.8 years) and untrained (108 participants, 43 girls; age: 14.7 ± 1.7 years) adolescents completed an incremental ramp test to exhaustion during which breath by gas exchange, beat-by-beat heart rate (HR), stroke volume (SV) and cardiac output (Q·) and muscle deoxygenation were assessed. Device-based physical activity was also assessed over seven consecutive days. Boys, irrespective of training status, had a significantly higher absolute (2.65 ± 0.70 L min−1 vs. 2.01 ± 0.45 L min−1, p < 0.01) and allometrically scaled (183.8 ± 31.4 mL·kg−b min−1 vs. 146.5 ± 28.5 mL·kg−b min−1, p < 0.01) peak oxygen uptake (V·O2) than girls. There were no sex differences in peak HR, SV or Q· but boys had a higher muscle deoxygenation plateau when expressed against absolute work rate and V·O2 (p < 0.05). Muscle deoxygenation appears to be more important in determining the sex differences in peak V·O2 in youth. Future research should examine the effects of sex on the response to different training methodologies in youth.