Purpose: To compare the time-course change in the postoperative anorectal function between laparoscopic intersphincteric resection (ISR) and low anterior resection (LAR). Methods: This is a single-institution observational study. We evaluated the time-course change in the anorectal function using functional questionnaires before and at 6, 12, and 24 months after laparoscopic ISR or LAR. Results: Sixty-two patients answered the functional questionnaires (28 in the ISR group and 34 in the LAR group). In the ISR group, the Wexner scores at 6, 12, and 24 months postoperatively were significantly higher than preoperatively. Importantly, the Wexner score at 24 months postoperatively was significantly lower than that at 6 months postoperatively. The low GIFO scores at 6 and 12 months postoperatively tended to be recovered to some extent at 24 months postoperatively. In the LAR group, Wexner score at 6 months postoperatively was significantly higher than that preoperatively. Notably, the Wexner score at 12 months postoperatively was recovered to almost the same as that preoperatively. The GIFO scores at 12 months postoperatively were mostly recovered to the same levels as those preoperatively. Conclusions: Laparoscopic ISR exhibits different time-course changes in the anorectal function from laparoscopic LAR.