Multidisciplinary lifestyle interventions for children with obesity in Denmark often include recommendations regarding physical activity, but no structured exercise program. We hypothesized that adding high-intensity interval training (HIIT) to a multidisciplinary lifestyle intervention would improve BMI z-score (primary outcome), waist circumference, blood pressure, and health-related quality of life (HRQOL). This randomized controlled trial included 173 children and adolescents with obesity. Participants were allocated to 12-months lifestyle intervention (N = 83), or 12-month lifestyle intervention accompanied by a 12-week HIIT program (N = 90). HIIT consisted of three weekly sessions and included activities eliciting intensities >85% of maximal heart rate. Attendance rate for the 3-months HIIT intervention was 68.0 ± 23.2%. Dropout was lower in HIIT compared to control at three months (7.8% vs. 20.5%) and 12 months (26.5% vs 48.2%). Changes in BMI z-score did not differ between HIIT and control at 3 months (Mean Difference (MD): 0.01, 95% confidence interval (CI): -0.09; 0.12, P = 0.82) or 12 months (MD: 0.06, CI: -0.07;0.19, P = 0.34). Across randomization, BMI z-score was reduced by 0.11 (CI: 0.17; 0.06, P < 0.01) at 3 months and 0.20 (CI: 0.26;0.14, P < 0.01) at 12 months. At 3 months, HIIT experienced a greater increase in HRQOL of 2.73 (CI: 0.01;5.44, P = 0.05) in PedsQL Child total-score and 3.85 (CI: 0.96; 6.74, P < 0.01) in psychosocial health-score compared to control. At 12 months, PedsQL Child physical-score was reduced by 6.89 (CI: 10.97; 2.83, P < 0.01) in HIIT compared to control. No group differences or changes over time were found for waist circumference or blood pressure. Adding a 12-week HIIT program did not further augment the positive effects of a 12-month lifestyle intervention on BMI z-score. Adding HIIT improved HRQOL after 3 months, but reduced HRQOL at 12 months. Implementation of HIIT in community-based settings was feasible and showed positive effects on adherence to the lifestyle intervention.