Adequate oncological outcomes have been demonstrated with rectal resection and handsewn coloanal anastomosis (CAA) in tumours in close proximity to the internal anal sphincter. Our aim was to assess functional differences between handsewn CAA and ultralow stapled anastomosis. Participants were identified from a single-surgeon series. Included participants underwent anorectal physiology testing of anal sphincter function, in addition to completion of several questionnaires: Wexner Incontinence Score (WIS); Birmingham Bowel, Bladder and Urinary Symptom Questionnaire (BBUSQ); Low Anterior Resection Syndrome (LARS) Score; SF36. Non-parametric data compared using the Mann-Whitney U test. 20 participants were included; 11 stapled and 9 handsewn. Mean follow-up was 2.95 ± 1.97 years. The mean LARS score was 21.9 ± 1.97 years in the stapled group versus 29.4 ± 9.57 in the handsewn group (p = 0.133). The Wexner incontinence score was significantly higher in the handsewn group (p = 0.0076), with a mean score of 4.6 ± 3.69 versus 10.9 ± 4.76. The incontinence domain of the BBUSQ was also significantly worse in patients with a handsewn anastomosis (p = 0.001). With the exception of general health (p = 0.035) and social functioning (p = 0.035), which were worse in the handsewn groups, the other six domains of the SF-36 showed no statistical difference between groups. Anorectal physiology scores were not significantly different. Handsewn CAA anastomosis is known to be safe and oncologically feasible. Patient selection should be vigorous, with preoperative counseling regarding the likelihood of incontinence to manage patients' expectations and promote comparable quality of life in the long-term.