Peptic ulcer disease is a common gastrointestinal tract disorder that affects up to 20% of the population of the world. Treatment of peptic ulcer remains challenging due to the limited effectiveness and severe side effects of the currently available drugs. Hence, natural compounds, owing to their medicinal, ecological, and other safe properties, are becoming popular potential candidates in preventing and treating peptic ulcers. Flavonoids, the most abundant polyphenols in plants, exhibit gastroprotective effects against peptic ulcer both in vivo and in vitro. In this review, we summarized the anti-ulcer functions and mechanisms, and also the bioavailability, efficacy, and safety, of flavonoid monomers in the gastrointestinal tract. Flavonoids exerted cytoprotective and rehabilitative effects by not only strengthening defense factors, such as mucus and prostaglandins, but also protecting against potentially harmful factors via their antioxidative, anti-inflammatory, and antibacterial activities. Although controlled clinical studies are limited at present, flavonoids have shown a promising preventable and therapeutic potential in peptic ulcers.