Background Ulcerative colitis (UC) is a form of inflammatory bowel disease (IBD). There are several chemical and herbal drug regimens for treatment of UC. Objectives The aims of this study were to investigate the effects of Hypericum perforatum on histopathological and tissue malondialdehyde (MDA) level of colonic tissue in rat with induced UC. Materials and Methods Two milliliters of 3% acetic acid was administered into the colon to induce UC. Seventy rats were divided into seven equal groups. Groups I and II received 1 mL of 600 and 300 mg/kg H. perforatum extract orally per day respectively; groups III and IV received 1 mL of 20% and 10% intra-colonic gel form of H. perforatum extract daily respectively; group V as positive control received 2 mL of intra-colonic asacol; group VI was a negative control receiving 0.5 mL/kg of normal saline after induction of UC; group VII received just intra-colonic gel base. All the animals were evaluated for histological changes and tissue MDA level seven days after the treatment. Results H. perforatum extract in the two forms of trans-rectal and oral administration on the seventh day after the therapy could result in a more healing effect on acetic acid-induced damaged colonic tissue with a reduction in the MDA activity. In trans-rectal administration, the 20% gel form had a better healing response than the 10% gel form and was prominently more effect on the seventh day of the therapy. In oral administration of strawberry extract, the 600 mg/kg dosage had a better healing response than the 300 mg/kg and was significantly more effective on the seventh day of therapy. Conclusions So H. perforatum may be considered as a treatment of choice for UC especially in gel form to broaden the current therapy options of the disease.