Rectourethral fistula is one of the complications that can occur after prostatectomy in the urologic discipline. However, a delayed-onset rectourethral fistula after intersphincteric resection (ISR) for low rectal cancer is extremely rare. Here, we report one such case in a 57-year-old man. After ISR for low rectal cancer with a diverting stoma (DS), the DS was closed. After approximately 1 year, frequent pneumaturia and right orchitis were observed. Results of contrast enemas and abdominal computed tomography examinations revealed a rectourethral fistula from an anastomosis to the urethra. The colonoscopic appearance revealed a pinhole fistula on the anastomotic line, with thick pus. We performed a transverse colostomy, and the pneumaturia and right orchitis were no longer observed. Two months later, colonoscopy, contrast enemas, and cystoscopy revealed no rectourethral fistula. To the best of our knowledge, our case is the first report of a delayed-onset rectourethral fistula after ISR.