Advances in the pharmacological treatment of ulcerative colitis (UC) have enormously decreased the frequency of emergent surgeries. Ileal pouch-anal anastomosis (IPAA) is the procedure of choice in surgical treatment of refractive UC and J-pouch configuration is by far the most preferred pouch design by surgeons. Pouch configuration probably influences the outcomes of the surgery. In this study, we compared the impact of J-pouch size on the functional and quality of life (QoL) outcomes of patients. In this prospective cohort study, we recruited patients who underwent IPAA in two referral centers of our university with two different J-pouch sizes. Demographic data of patients were collected using the patients' medical files. To assess the QoL and bowel function status, SF-36 and Öresland scores were used to evaluate patients 6 and 12 months after the operation. Data analysis was performed with SPSS ver 21. 62 patients were evaluated in the study (31 subjects in each group). The mean age of patients was 40.85 ± 12.98. Thirty-nine patients (60.0%) were males and 23 (35.9%) were females. The mean of SF-36 and Öresland score was 84.30 ± 13.39 and 3.33 ± 2.45, respectively. The mean of SF-36 was significantly higher in patients with shorter J-pouch (P value 0.00). The mean of Öresland score was relatively lower in patients with shorter J-pouch but the difference was not statistically significant (P value 0.06). QoL was correlated with bowel functional outcomes and shorter length of the J-pouch. The only demographic parameter that was correlated with QoL was body mass index.