Background: Bojanggunbi-tang (BGT) is a well-known combination of ancient Korean herbal medicines and has been widely used for treating gastrointestinal symptoms. Objectives: This study was aimed at investigating whether BGT protects against non-steroidal anti-inflammatory drug (NSAID)-induced small intestinal injury (NSI), by using a murine model of indomethacin-induced NSI. Materials and Methods: NSI was induced in the mice by subcutaneous injections of 15 mg/kg indomethacin. BGT was administered at doses of 50, 150, and 450 mg/kg, while the positive control received sodium alginate. The treatments were orally administered twice, 30 min before and 6 h after the induction of NSI. The body weight, length of small intestine, macroscopic damages, and histological damages were assessed after 24 h of induction. Results: Gross anatomical analysis revealed that BGT inhibited the shortening of the small intestine and reduced the area of ulceration. Histological analysis revealed that BGT lowered the ulceration and inflammation scores. However, there was no difference between the groups with respect to weight loss. Conclusion: BGT ameliorated NSI via its anti-inflammatory and anti-ulcerative properties. The current study suggests that BGT could be a therapeutic option for NSI.