Background: Ileal pouch-anal anastomosis (IPAA) is the procedure of choice in patients with ulcerative colitis (UC) requiring surgery. Advantages of laparoscopic IPAA (lap-IPAA) compared to open surgery have been investigated. However, laparoscopic dissection in the pelvis is still a challenge. A transanal approach provides better access to lower pelvis and avoids multiple staple firings, which could reduce the risk of anastomotic complications. The aim of this study was to compare short-term outcomes of transanal proctectomy with IPAA (ta-IPAA) with conventional lap-IPAA in patients with UC. Methods: A single-center retrospective study was conducted on consecutive UC patients, treated at Copenhagen University Hospital, Hvidovre, undergoing either laparoscopic or transanal IPAA in the period between January 2013 and December 2020. Exclusion criteria were Crohn’s disease, previous extensive abdominal surgery and impaired sphincter function. Primary outcomes were overall postoperative complications. Secondary outcomes were length of hospital stay and re-admissions. For comparison between ta-IPAA and lap-IPAA, the Mann–Whitney U test was used for continuous variables, and Chi-square and Fisher’s exact test for categorical variables. Results: A total of 65 patients with ta-IPAA (34 males, 31 females, median age 31 years [range 12–66 years]) and 70 patients with lap-IPAA (35 males, 35 females, median age 26 years [range 12–66 years]) were included. There was no difference between ta-IPAA and lap-IPAA regarding age, sex, body mass index or American Society of Anesthesiologists class. The primary colectomy procedure was performed laparoscopically in 95% of the ta-IPPA and 91% of the lap-IPAA patients (p = 0.493). The mean time between total colectomy and IPAA was 15 and 9 weeks for ta-IPAA and lap-IPAA, respectively (p = 0.048). A higher proportion of patients with ta-IPAA were treated with biologics preoperatively (98 vs. 82%; p = 0.002). Patients with ta-IPAA had a significantly higher mean operative time compared to lap-IPAA (277 min vs. 224 min; p = 0.001). There was no difference in the overall postoperative complication rate (ta-IPAA: 23% vs. lap-IPAA: 23%; p = 0.99). Pouch-related complications occurred in 13% of the ta-IPAA patients and 29% of lap-IPPA patients (p = 0.402). There was no difference in the anastomotic leakage rates. Readmission rates were similar in the ta-IPAA and lap-IPAA group (26 vs. 29%; p = 0.85), including IPAA-related readmissions. The mean follow-up time was 24 and 75 months for ta-IPAA and lap-IPAA, respectively (p = 0.001), and the ileostomy closure rate was similar in both groups of patients (p = 0.96). Conclusions: The ta-IPAA approach for UC is a safe procedure and offers acceptable short-time outcomes.