The aim of the present study was to evaluate the short-term surgical outcomes of laparoscopic intersphincteric resection (ISR) for a lower rectal tumor in comparison with a case-control series of patients undergoing open ISR. Quality of life factors and anal function were also evaluated. Between July 2008 and April 2013, 103 patients with lower rectal cancer underwent laparoscopic surgery at the Surgical Oncology Department of Gifu University School of Medicine. A total of 25 patients with lower rectal cancer underwent ISR, and 19/25 patients who underwent laparoscopic ISR were compared with the control group of 6 patients who underwent open ISR. The technical feasibility and safety of ISR, and the short- and long-term outcomes following laparoscopic ISR were evaluated. Additional data associated with fecal incontinence conditions of the postoperative patients were evaluated using the Modified Fecal Incontinence Quality of Life scale. There was no recorded perioperative mortality, three complications were observed to occur in three patients and the morbidity rate was 15.8%. The postoperative complications detected included bleeding in one patient and ileus in two patients of the laparoscopic ISR group. The rate of severe complications of grade ≥3a was 15.8% and that of grade ≥3b was 5.3%. In the matched case-control study, blood loss was significantly lower in the laparoscopic ISR group. The median postoperative hospital stay was 14.1 days in the laparoscopic ISR group, which was significantly shorter compared with in the open ISR group (18.7 days). Cancer recurrence was detected in one (5%) patient in a single inguinal lymph node. No significant differences between the ISR and ultra-low anterior resection (ULAR) groups were observed in the maximum resting and maximum squeeze pressures; the outcomes for anal function and fecal incontinence were the same for ISR and ULAR. Thus, laparoscopic ISR for lower rectal cancer may provide a benefit in the early postoperative period without increasing morbidity or mortality.