Sphincter-saving surgery (SSS) is the gold standard for rectal cancer surgery but results in a wide spectrum of bowel dysfunction. This study investigated the impact of colonic dysmotility on the incontinent form of bowel dysfunction. Bowel function of patients who received SSS with loop ileostomy for treating rectal cancer was reviewed retrospectively from June 2013 two August 2015 at a single hospital. Immediately after closure of a diverting stoma, patients were tested for the colonic transit time (CTT) using radiopaque markers. Bowel dysfunction at 6 and 12 months after SSS was measured as the severity of fecal incontinence according to the Cleveland Clinic Incontinence Score (CCIS) and the use of an anti-diarrheal drug. A short CTT for the left colonic segment was significantly associated with the high CCIS and use of an antidiarrheal agent at 6 months after sphincter preservation. However, the CTT didn’t correlate with the CCIS at 12 months after SSS. Rather, age and surgical method demonstrated a significant association. Colonic dysmotility after SSS appears to intensify fecal incontinence for a relatively short period. Its impact abates within a year.