(1) Background: The determination of body composition is an important method to investigate patients with obesity and to evaluate the efficacy of individualized medical interventions. Bioelectrical impedance-based methods are non-invasive and widely applied but need to be validated for their use in young patients with obesity. (2) Methods: We compiled data from three independent studies on children and adolescents with obesity, measuring body composition with two bioelectrical impedance-based devices (TANITA and BIACORPUS). For a small patient group, additional data were collected with air displacement plethysmography (BOD POD) and dual-energy X-ray absorptiometry (DXA). (3) Results: Our combined data on 123 patients (age: 6–18 years, body mass index (BMI): 21–59 kg/m²) and the individual studies showed that TANITA and BIACORPUS yield significantly different results on body composition, TANITA overestimating body fat percentage and fat mass relative to BIACORPUS and underestimating fat-free mass (p < 0.001 for all three parameters). A Bland–Altman plot indicated little agreement between methods, which produce clinically relevant differences for all three parameters. We detected gender-specific differences with both methods, with body fat percentage being lower (p < 0.01) and fat-free mass higher (p < 0.001) in males than females. (4) Conclusions: Both bioelectrical impedance-based methods provide significantly different results on body composition in young patients with obesity and thus cannot be used interchangeably, requiring adherence to a specific device for repetitive measurements to ascertain comparability of data.