Background. Mechanical efficiency (ME) might be an important parameter evaluating cardiometabolic health and the effectiveness of physical activity interventions in individuals with obesity. However, whether these cardiometabolic risk factors may relate to ME in adolescents with obesity is not known yet. Therefore, this study aims to compare the mechanical efficiency during maximal exercise testing between adolescents with obesity and lean adolescents, and to examine associations with exercise tolerance and metabolic health. Methods. Twenty-nine adolescents with obesity (BMI SDS: 2.11 ± 0.32, age: 13.4 ± 1.1 years, male/female: 15/14) and 29 lean (BMI SDS: −0.16 ± 0.84, age: 14.0 ± 1.5 years, male/female: 16/13) adolescents performed a maximal cardiopulmonary exercise test from which the net mechanical efficiency (MEnet) and substrate oxidation (carbohydrates and lipids) were calculated. Indicators for peak performance were collected. Biochemistry (lipid profile, glycaemic control, inflammation, leptin) was studied in fasted blood samples. Regression analyses were applied to examine relations between MEnet and exercise tolerance or blood variables in the total group. Results. Peak work rate (WRpeak), oxygen uptake (V˙O2peak)/WRpeak, ME, and MEnet were significantly lower (p < 0.05) in adolescents with obesity compared to their lean counterparts (p < 0.05). Furthermore, a reduced MEnet was independently related to a lower WRpeak (SC β = 2.447; p < 0.001) and elevated carbohydrate oxidation during exercise (SC β = −0.497; p < 0.001), as well as to elevated blood low-density lipoprotein cholesterol (SC β = −0.275; p = 0.034) and fasting glucose (SC β = −0.256; p = 0.049) concentration. Conclusion. In adolescents with obesity, the mechanical efficiency is lowered during exercise and this relates to exercise intolerance and a worse metabolic health.