Background Little is known about the long-term outcomes of bariatric surgery for severe adolescent obesity, raising questions about the durability of early responses to surgery. We aimed to analyse long-term (>5 years) outcomes of Roux-en-Y gastric bypass in a cohort of young adults who had undergone the operation during adolescence, in the Follow-up of Adolescent Bariatric Surgery at 5 Plus Years (FABS-5+) extension study. Methods A cohort of young people aged 13–21 years underwent Roux-en-Y gastric bypass for clinically severe obesity at a paediatric academic medical centre in the USA. We did a prospective follow-up analysis of these patients' outcomes 5–12 years after surgery. Outcomes assessed included BMI, comorbidities, micronutrient status, safety, and other risks. The FABS study is registered with ClinicalTrials.gov, number NCT00776776. Findings Between May, 2001, and February, 2007, 74 young people underwent Roux-en-Y gastric bypass in the FABS study. Of these, 58 individuals were eligible for the FABS-5+ study, could be located, and agreed to follow-up assessment. At baseline, the mean age of the cohort was 17·1 years (SD 1·7) and mean BMI was 58·5 kg/m2 (10·5). At mean follow-up of 8·0 years (SD 1·6; range 5·4–12·5), the mean age of the cohort was 25·1 years (2·4) and mean BMI was 41·7 kg/m2 (12·0; mean change in BMI −29·2% [13·7]). From baseline to long-term follow-up, significant declines were recorded in the prevalence of elevated blood pressure (27/57 [47%] vs 9/55 [16%]; p=0·001), dyslipidaemia (48/56 [86%] vs 21/55 [38%]; p<0·0001), and type 2 diabetes (9/56 [16%] vs 1/55 [2%]; p=0·03). At follow-up, 25 (46%) of 58 patients had mild anaemia (ie, not requiring intervention), 22 (45%) had hyperparathyroidism, and eight (16%) had low amounts of vitamin B12 (ie, below the normal cutpoint). Interpretation Roux-en-Y gastric bypass surgery resulted in substantial and durable bodyweight reduction and cardiometabolic benefits for young adults. Long-term health maintenance after Roux-en-Y gastric bypass should focus on adherence to dietary supplements and screening and management of micronutrient deficiencies. Funding Ethicon Endosurgery, National Center for Advancing Translational Sciences (US National Institutes of Health).