The capacity to match carbohydrate (CHO) oxidation with CHO availability (deemed metabolic flexibility (MetFlex)) may be important for type 2 diabetes prevention. In adults, impaired MetFlex is associated with insulin resistance (IR), which can be improved with as little as 7 days of exercise. Whether this occurs similarly in children is unknown. We hypothesized that 7 consecutive days of exercise would improve MetFlex and IR in children with obesity. Twelve children (8 boys, 4 girls) completed 2 study visits before (PRE) and 2 study visits after (POST) exercise training. At visit 1, fasting blood was collected, and anthropometry and maximal oxygen uptake were assessed. At visit 2, a 13C-enriched CHO drink was ingested before exercise (3 × 20 min) at ∼59% maximal oxygen uptake. Exogenous CHO oxidative efficiency, used as a surrogate measurement of MetFlex, was calculated from breath samples. During training, participants alternated between continuous and high-intensity interval cycling sessions at home under supervision. In spite of good training adherence, there was no improvement in MetFlex (PRE: 20.7% ± 1.8%, POST: 18.9% ± 4.9%, p = 0.22) or homeostasis model assessment of insulin resistance (PRE: 8.7 ± 4.6, POST: 8.1 ± 6.0, p = 0.51). Future research should investigate exercise volume, sex, and pubertal effects on the early responsiveness of MetFlex to exercise therapy.