Background Laparoscopic ileal pouch–anal anastomosis (IPAA) technique is not standardized. An irregular division of the rectum could result in poor functional outcomes and residual diseased mucosa. The aim of the study was to develop a new technique for performing the rectal transection via a laparoscopic approach, and to compare the outcomes of this technique with those of the open surgery IPAA. Methods This prospective study included all patients who underwent restorative proctectomy (following a previous subtotal colectomy) for ulcerative colitis in October 2017–November 2020. Rectal division was performed using a 30 mm open linear stapler which was applied laparoscopically across the distal rectum. Postoperative and functional outcomes, length of anal stump and completeness of mucosal removal were compared. Only the patients who had their ileostomy reversed by 31 December 2020 and, therefore, a minimum follow-up of 6 months from the ileostomy closure, were included in the analysis of the functional outcomes and quality of life. Results There were 207 patients (161 laparoscopic, 46 open). Median age was 43 (18–77) years and 85 patients (41.1%) were male. Major complications (9.3 vs. 8.7%, p  = 0.89) including anastomotic leaks (3.7 vs 4.4%, p  = 0.84) were similar after laparoscopic and open IPAA. Patients reported a comparable number of bowel movements during the day (6 vs. 7, p  = 0.21) and at night (2 vs. 2, p  = 0.66), and a similar rate of episodes of incontinence during the previous 6 months (3.7 vs. 4.3%, p  = 0.75). The mean Cleveland Global Quality of Life score was also similar (0.79 vs. 0.74, p  = 0.35). Conclusion Our technique is safe and reproducible, and replicates the results of the open IPAA, while maintaining the advantages of minimally invasive surgery and avoiding any kind of anal manipulation which could result in poor long-term functional outcomes.