Background: To clarify the pudendal motor (PMN) and sensory (PSN) nerves play in preventing fecal incontinence (FI) after low anterior resection (LAR) for lower rectal cancer, the PMN and PSN functions were studied. Methods: Sixty patients were divided into groups A (n = 20, FI) and B (n = 40, continence). These were compared with group C (n = 30, control subjects). PMN latency (PMNL) (right, left, and posterior sides of the anal canal) was studied by sacral magnetic stimulation. Anal mucosal electric sensitivity (AMES) was measured at the lower, dentate line (DL), and upper zones. Results: The distance of anastomosis from anal verge (DAAV) in group A was significantly shorter than in group B (p value < 0.001). In PMNL, the conduction delay in group A was significantly longer than in groups B and C at all sides (p value < 0.001, respectively). On AMES, the sensitivity of patients in group A was significantly lower than in groups B and C at all zones (p value < 0.001, respectively). In groups A, B, and C, correlation coefficients between SMNL (posterior side) and AMES (DL zone) were 0.780, 0.858, and 0.793, respectively (p value < 0.001). Conclusion: FI after LAR with a short DAAV may lead to external anal sphincter dysfunction due to damage of both PMN and PSN.