Background Recent data support the use of bariatric surgery in adolescents with severe obesity following unsuccessful non-surgical treatments. Sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (RYGB) have demonstrated reasonably similar weight loss and reduction of obesity related comorbidities in randomized trials in adults. SG has internationally become the most commonly used procedure in adolescents, yet long-term outcome data are lacking. No randomized controlled trial comparing SG and RYGB has been performed in adolescents. Objective Determine whether SG is non-inferior to RYGB in terms of total body weight (TBW) loss in adolescents with severe obesity. Methods A multicenter randomized controlled non-inferiority trial. Two hundred sixty-four adolescents aged 13-17 (Tanner stage >= IV) with severe obesity (corrected for age and sex) will be included. Adolescents agreeing to participate will be randomized to either RYGB or SG. The primary outcome is the proportion of participants achieving 20% TBW loss at 3 years postoperatively. Secondary outcomes include (i) change in body weight, body mass index (BMI) and BMI standard deviation score, (ii) incidence of adverse health events and need for additional surgical intervention, (iii) resolution of obesity-related comorbidities, (iv) prevalence of cardio metabolic risk factor measures, (v) bone health measures and incidence of bone fractures, (vi) quality of life including psychosocial health, patient satisfaction and educational attainment and (vii) body composition. Follow-up will extend into the long term. Results Not applicable. Discussion This study will, to our knowledge, be the first randomized controlled trial comparing SG and RYGB in adolescents with severe obesity.