We aimed to evaluate the efficacy of treatment with partially hydrolyzed guar gum (PHGG) using a rat model of ileal pouch-anal anastomosis and pouchitis. In the J pouch groups, tissue myeloperoxidase activities were significantly higher than native myeloperoxidase activities (P = 0.020; P = 0.015; P = 0.004, respectively). A statistically significant difference in total histological score was detected in the J pouch + 5% dextran sulfate sodium (DSS) group, compared to the J pouch control and the J pouch + 5% DSS + PHGG groups (P < 0.01 and P < 0.01, respectively). There was a significant overgrowth of aerobes and anaerobes in the J pouch + 5% DSS group. This study demonstrated that rectal administration of PHGG attenuates the severity of pouchitis in a rat model. In conclusion, PHGG may be an additional therapeutic strategy for the treatment of pouchitis.