Marginal ulcer is a significant complication of laparoscopic Roux-en-Y gastric bypass (LRYGB). Most marginal ulcers resolve with medical management, but nonhealing ulcers may require revision of the gastrojejunostomy, a procedure with significant morbidity and mortality. Traditionally, surgical therapy for refractory peptic ulcers includes a vagotomy. The current study evaluates the effectiveness of thoracoscopic truncal vagotomy (TTV) in the management of refractory marginal ulcers. All patients at two institutions with an intractable marginal ulcer after LRYGB treated with TTV between 2003 and 2010 were reviewed. Data were collected from chart review and telephone interview. Seventeen patients (mean age, 39 ± 13 years; 16 females) were diagnosed with marginal ulceration a median of 18 months after LRYGB and proceeded to TTV at a mean of 39 ± 43 weeks (range, 1 to 114 weeks) after the diagnosis. The median operative time was 89 ± 65 minutes (range, 45 to 318 minutes). Four patients had a complication (sympathetic contralateral pleural effusion, pneumothorax, operative bleeding, and readmission for emesis). Eleven patients had follow-up of 3 months to 6 years (median, 7 months). Nine patients (82%) had symptomatic improvement and/or endoscopic resolution, whereas two (18%) did not. No patient had endoscopic evidence of persistent or recurrent marginal ulcer. TTV achieves symptomatic improvement and/or endoscopic resolution of intractable marginal ulcers in over 80 per cent of patients status post gastric bypass and therefore offers a less morbid alternative to revision of the gastrojejunostomy.