Purpose: Faecal incontinence is common in persons with severe obesity. Little is known about how the thicknesses of the internal anal sphincter (IAS) and the external anal sphincter (EAS) change in relation to weight loss following metabolic bariatric surgery (MBS). This study aims to investigate any change in IAS and EAS thickness 6 months after Roux-en-Y gastric bypass surgery (RYGB) and to determine whether any such change correlates with a change in faecal incontinence pattern. Methods: Thirty-one patients underwent three-dimensional endoanal ultrasound to measure anal sphincter thickness before and 6 months after RYGB. Patients completed the validated Wexner and LARS (low anterior resection syndrome) questionnaires at the same time to evaluate any change in faecal incontinence and urgency symptoms following surgery. Results: No significant change in the thicknesses of the IAS and EAS was seen. The Wexner score decreased from 18 to 13 (less incontinence). Conversely, the number of patients with LARS increased from 10 to 15 six months after surgery (more urgency). Conclusion: RYGB had no effect on the thickness of the anal sphincter 6 months after surgery. However, the pattern of faecal incontinence changed, with a decrease in leakage and whole faecal incontinence and an increase in urgency.