Pouchitis is one of the major postoperative complications of ulcerative colitis (UC), and it is still difficult to predict the development of pouchitis after ileal pouch-anal anastomosis (IPAA) in UC patients. In this study, we examined whether a deep learning (DL) model could predict the development of pouchitis. UC patients who underwent two-stage restorative proctocolectomy with IPAA at Keio University Hospital were included in this retrospective analysis. The modified pouchitis disease activity index (mPDAI) was evaluated by the clinical and endoscopic findings. Pouchitis was defined as an mPDAI ≥ 5.860; endoscopic pouch images before ileostomy closure were collected. A convolutional neural network was used as the DL model, and the prediction rates of pouchitis after ileostomy closure were evaluated by fivefold cross-validation. A total of 43 patients were included (24 males and 19 females, mean age 39.2 ± 13.2years). Pouchitis occurred in 14 (33%) patients after ileostomy closure. In less than half of the patients, mPDAI scores matched before and after ileostomy closure. Most of patients whose mPDAI scores did not match before and after ileostomy closure had worse mPDAI scores after than before. The prediction rate of pouchitis calculated by the area under the curve using the DL model was 84%. Conversely, the prediction rate of pouchitis using mPDAI before ileostomy closure was 62%. The prediction rate of pouchitis using the DL model was more than 20% higher than that using mPDAI, suggesting the utility of the DL model as a prediction model for the development of pouchitis. It could also be used to determine early interventions for pouchitis.