Intersphincteric resection (ISR) is a surgical technique intended to avoid abdominoperineal resection (APR) in patients diagnosed with low-lying rectal cancer. However, the oncologic outcomes of minimally invasive ISR are still controversial. We analyzed the long-term oncologic outcomes of open and minimally invasive ISR. A total of 313 rectal cancer patients who underwent ISR between 2000 and 2014 were analyzed, including 147 in the open surgery group and 166 in the minimally invasive surgery (MIS) group. This study also analyzed 113 patients who received neoadjuvant chemoradiotherapy (nCRT) for advanced lower rectal cancer. Propensity score matching (PSM) was used to correct for differences between the two groups. 5-year disease-free survival (DFS) rate was the primary end point. The length of hospital stay was significantly shorter in the MIS group (9.6 vs. 11.8 days, p < 0.001). Differences in overall postoperative morbidity rates between the groups were not significant; however, the rate of surgical site infection was significantly lower in the MIS group (1.2 vs. 10.9%, p < 0.001). The 5-year DFS associated with all stages combined in the matched patients were not significantly different: 75.2% in the open group vs. 64.2% in the MIS group (p = 0.214). Similar results were found in matched patients treated with nCRT, with 72.0% in the open group and 61.3% in the MIS group (p = 0.078) showing DFS. Both minimally-invasive and open ISR for rectal cancer yielded similar 5-year oncologic outcomes. MIS showed statistically significant advantages in some postoperative outcomes such as reduced surgical site infection and shorter hospital stay, and similar long-term outcomes compared with open ISR. This study also suggests that MIS after nCRT for advanced rectal cancer represents a surgical option with similar oncological results.