Background and Objectives: The objective of this article is to evaluate the long-term oncological and functional outcomes following modified intersphincteric resections (ISR) for low rectal cancer. The modified technique consisted of the abandonment of colonic J-pouches, transverse coloplasty, or defunctioning temporary stoma in favor of a direct handsewn coloanal anastomosis (CAA). Material and Methods: Sixty consecutive patients with type II and III (juxta-anal or intra-anal) low rectal tumors underwent modified ISR by the same surgical team and were followed for a period of five years. Functional outcomes using the Wexner Score, postoperative complications, recurrence rates, morbidity, and mortality rates were assessed. Results: The five-year survival rate was 93.3% with a disease-free interval at three years of 98%. Morbidity was 15% (n = 9) consisting of intestinal wall necrosis (n = 6), stenosis (n = 2), and sacral metastasis (n = 1). The Wexner score values were, at 1 year, 8.5 (range, 4–13); at three years 7.2 (range, 2–11); and at 5 years 6.7 (range, 2–12). A second surgery was needed in only one case that showed postoperative transmural necrosis of the colonic wall. Conclusions: In highly selected patients with type II or III low rectal tumors and proper preoperative imaging staging, ISR might be a viable alternative to other techniques such as abdominoperineal resection and low anterior resection, both from a functional and an oncological perspective.