The principles of management are the same as for the chronic ulcer. The steps of management are similar as in erosive gastritis.

Endoscopic means of treating stress ulceration may be ineffective and operation required. It is believed that shunting of blood away from the mucosa makes the mucous membrane ischaemic and more susceptible to injury.

Treatment of stress ulceration usually begins with prevention. Careful attention to respiratory status, acid-base balance, and treatment of other illnesses helps prevent the conditions under which stress ulcers occur. Patients who develop stress ulcers typically do not secrete large quantities of gastric acid; however, acid does appear to be involved in the pathogenesis of the lesions. Thus it is reasonable either to neutralize acid or to inhibit its secretion in patients at high risk.

In case of severe hemorrhagic or erosive gastritis and stress ulcers, a combination of antacids and H2-blockers may stop active bleeding and prevent re bleeding. In selected patients, either endoscopic therapy or selective infusion of vasopressin into the left gastric artery may help control the hemorrhage.

The need for medications to prevent stress ulcer among those in the intensive care unit is unclear. As of 2014, the quality of the evidence is poor. It is unclear which agent is best or if prevention is needed at all. Benefit may only occur in those who are not being fed.

Possible agents include antacids, H2-receptor blockers, sucralfate, and proton pump inhibitors (PPIs). Tentative evidence supports that PPIs may be better than H2 blockers.

Concerns with the use of stress ulcer prophylaxis agents include increased rates of pneumonia and "Clostridium difficile" colitis.

It is diagnosed and treated endoscopically; however, endoscopic ultrasound or angiography can be of benefit.

Endoscopic techniques used in the treatment include epinephrine injection followed by bipolar or monopolar electrocoagulation, injection sclerotherapy, heater probe, laser photocoagulation, hemoclipping or banding. Alternatively, in patients with refractory bleeding Interventional Radiology may be consulted for an angiogram with subselective embolization.

The mortality rate for Dieulafoy's was much higher before the era of endoscopy, where open surgery was the only treatment option.

Antacids are a common treatment for mild to medium gastritis. When antacids do not provide enough relief, medications such as H blockers and proton-pump inhibitors that help reduce the amount of acid are often prescribed.

Cytoprotective agents are designed to help protect the tissues that line the stomach and small intestine. They include the medications sucralfate and misoprostol. If NSAIDs are being taken regularly, one of these medications to protect the stomach may also be taken. Another cytoprotective agent is bismuth subsalicylate.

Several regimens are used to treat "H. pylori" infection. Most use a combination of two antibiotics and a proton pump inhibitor. Sometimes bismuth is added to the regimen.

When "H. pylori" infection is present, the most effective treatments are combinations of 2 antibiotics (e.g. clarithromycin, amoxicillin, tetracycline, metronidazole) and a proton-pump inhibitor (PPI), sometimes together with a bismuth compound. In complicated, treatment-resistant cases, 3 antibiotics (e.g. amoxicillin + clarithromycin + metronidazole) may be used together with a PPI and sometimes with bismuth compound. An effective first-line therapy for uncomplicated cases would be amoxicillin + metronidazole + pantoprazole (a PPI).

H2 antagonists or proton-pump inhibitors decrease the amount of acid in the stomach, helping with healing of ulcers.

Healing is prolonged, and usually takes 6–10 weeks. The ulcer heals by secondary intention.

Corticosteroids are the mainstay of therapy with a 90% response rate in some studies. Appropriate duration of steroid treatment is unknown and relapse often necessitates long term treatment. Various steroid sparing agents e.g. sodium cromoglycate (a stabilizer of mast cell membranes), ketotifen (an antihistamine), and montelukast (a selective, competitive leukotriene receptor antagonist) have been proposed, centering on an allergic hypothesis, with mixed results. An elimination diet may be successful if a limited number of food allergies are identified.

The ulcers can be removed through fulguration (burned off with the use of electricity or a laser) or resection (cutting around the ulcer, removing both the ulcer and the surrounding inflamed tissue). Some ulcers may recur in the same location.

Many patients choose to live with the ulcers and treat the symptoms associated with them through bladder instillations and/or pain medication/therapy.

Patients with interstitial cystitis may find relief by modifying their diet to remove foods and beverages that trigger symptoms. Caffeinated beverages, particularly coffee (regular and decaf), tea, green tea, soda, artificial sugars and fruit juices. Cranberry juice may also trigger intense pain and discomfort. However, studies about the impact of specific foods and drinks on Hunner's ulcer symptoms are limited.

The first line therapy for aphthous stomatitis is topical agents rather than systemic medication, with topical corticosteroids being the mainstay treatment. Systemic treatment is usually reserved for severe disease due to the risk of adverse side effects associated with many of these agents. A systematic review found that no single systemic intervention was found to be effective. Good oral hygiene is important to prevent secondary infection of the ulcers.

Occasionally, in females where ulceration is correlated to the menstrual cycle or to birth control pills, progestogen or a change in birth control may be beneficial. Use of nicotine replacement therapy for people who have developed oral ulceration after stopping smoking has also been reported. Starting smoking again does not usually lessen the condition. Trauma can be reduced by avoiding rough or sharp foodstuffs and by brushing teeth with care. If sodium lauryl sulfate is suspected to be the cause, avoidance of products containing this chemical may be useful and prevent recurrence in some individuals. Similarly patch testing may indicate that food allergy is responsible, and the diet modified accordingly. If investigations reveal deficiency states, correction of the deficiency may result in resolution of the ulceration. For example, there is some evidence that vitamin B12 supplementation may prevent recurrence in some individuals.

The vast majority of people with aphthous stomatitis have minor symptoms and do not require any specific therapy. The pain is often tolerable with simple dietary modification during an episode of ulceration such as avoiding spicy and acidic foods and beverages. Many different topical and systemic medications have been proposed (see table), sometimes showing little or no evidence of usefulness when formally investigated. Some of the results of interventions for RAS may in truth represent a placebo effect. No therapy is curative, with treatment aiming to relieve pain, promote healing and reduce the frequency of episodes of ulceration.

Treatment is aimed at removing the irritant or infection. "Helicobacter pylori" infection is usually treated with antibiotics.

Treatment is cause-related, but also symptomatic if the underlying cause is unknown or not correctable. It is also important to note that most ulcers will heal completely without any intervention. Treatment can range from simply smoothing or removing a local cause of trauma, to addressing underlying factors such as dry mouth or substituting a problem medication. Maintaining good oral hygiene and use of an antiseptic mouthwash or spray (e.g. chlorhexidine) can prevent secondary infection and therefore hasten healing. A topical analgesic (e.g. benzydamine mouthwash) may reduce pain. Topical (gels, creams or inhalers) or systemic steroids may be used to reduce inflammation. An antifungal drug may be used to prevent oral candidiasis developing in those who use prolonged steroids. People with mouth ulcers may prefer to avoid hot or spicy foods, which can increase the pain. Self-inflicted ulceration can be difficult to manage, and psychiatric input may be required in some people.

Underlying cause of neuropathy is first treated. Necrotic portions of the wound are removed and wound is kept moist at associations. Infected ulcers are administered antibiotics.

Skin grafting is one of the options. It has been shown that ultrasound may increase the acceptance of graft at trophic ulcer sites.

In most people with peptic ulcer disease, the oedema will usually settle with conservative management with nasogastric suction, replacement of fluids and electrolytes and proton pump inhibitors.

Treatment for FAP depends on the genotype. Most individuals with the APC mutation will develop colon cancer by the age of 40, although the less-common attenuated version typically manifests later in life (40–70). Accordingly, in many cases, prophylactic surgery may be recommended before the age of 25, or upon detection if actively monitored. There are several surgical options that involve the removal of either the colon or both the colon and rectum.

- Rectum involved: the rectum and part or all of the colon are removed. The patient may require an ileostomy (permanent stoma where stool goes into a bag on the abdomen) or have an ileo-anal pouch reconstruction. The decision to remove the rectum depends on the number of polyps in the rectum as well as the family history. If the rectum has few polyps, the colon is partly or fully removed and the small bowel (ileum) can be directly connected to the rectum instead (ileorectal anastomosis).

- Rectum not involved: the portion of the colon manifesting polyps can be removed and the ends 'rejoined' (partial colectomy), a surgery that has a substantial healing time, but leaves quality of life largely intact.

Prophylactic colectomy is indicated if more than a hundred polyps are present, if there are severely dysplastic polyps, or if multiple polyps larger than 1 cm are present.

Treatment for the two milder forms of FAP may be substantially different from the more usual variant, as the number of polyps are far fewer, allowing more options.

Various medications are being investigated for slowing malignant degeneration of polyps, most prominently the non-steroidal anti-inflammatory drugs (NSAIDs). NSAIDS have been shown to significantly decrease the number of polyps but do not usually alter management since there are still too many polyps to be followed and treated endoscopically.

Antacids and sucralfate were found to be no better than placebo in a literature review. H2-RAs have been shown to have marked benefit in poor quality trials (30% relative risk reduction), but only a marginal benefit in good quality trials. Prokinetic agents would empirically seem to work well since delayed gastric emptying is considered a major pathophysiological mechanism in functional dyspepsia. They have been shown in a meta-analysis to produce a relative risk reduction of up to 50%, but the studies evaluated to come to this conclusion used the drug cisapride which has since been removed from the market (now only available as an investigational agent) due to serious adverse events such as torsades, and publication bias has been cited as a potential partial explanation for such a high benefit. Modern prokinetic agents such as metoclopramide, erythromycin and tegaserod have little or no established efficacy and often result in substantial side effects. Simethicone has been found to be of some value, as one trial suggests potential benefit over placebo and another shows equivalence with cisapride. So, with the somewhat recent advent of the proton pump inhibitor (PPI) class of medications, the question of whether these new agents are superior to traditional therapy has arisen.

Currently, PPIs are, depending on the specific drug, FDA indicated for erosive esophagitis, gastroesophageal reflux disease (GERD), Zollinger-Ellison syndrome, eradication of H. pylori, duodenal and gastric ulcers, and NSAID-induced ulcer healing and prevention, but not functional dyspepsia. There are, however, evidence-based guidelines and literature that evaluate the use of PPIs for this indication. A helpful chart summarizing the major trials is available from the functional dyspepsia guidelines published in the World Journal of Gastroenterology in 2006.

Diagnostic measures can be used as interventions to help stop bleeding in some cases. Bleeding that occurs due to a neoplasm (cancer growth) can be treated using colonoscopy and clipping, surgical intervention, or other measures, depending on the form and stage of cancer. Similarly, gastric cancer is treated depending on the staging, although typically requires surgical and medical therapy.

The treatment for motility issues, namely constipation, is typically to improve the movement of waste though the GI tract. This is done by using stool softeners (which work by pulling water into the stool while in the colon), addition of fiber to the diet, and use of osmotic laxatives (which help fluid movement through the colon, improving overall motility). Improving a persons gut motility can reduce the straining during defection and decrease the risk of developing of anal fissures. Anal fissures are associated with pain and blood on the toilet paper, and require time for healing. Treatment includes topical nitrates or calcium channel blockers and surgical interventions for chronic or complex cases. Similar to anal fissures, internal hemorrhoids can cause blood on the tissue when wiping, and be felt at the opening of the anus. Treatment options for hemorrhoids can be dependent on whether an underlying cause exists. An anorectal varices related hemorrhoids caused by cirrhosis, however symptomatic treatment often involves removal.

Colitis can be divided into infectious and drug induced, as can the treatment for these conditions. With infectious colitis, treatment is pathogen dependent, and generally requires the use of antibiotics. With drug-induced colitis, treatment typically involves removal of the offending agent, as is the case in NSAID induced PUD, however, removing radiation from a cancer patient is not always practical within a treatment regimen, so medical treatment is the primary mode of treatment.

Structural compromise leading to blood in stool is caused by a variety of conditions, and therefore requires different treatment for each condition. Peptic ulcer disease alone can be divided into multiple causes, but is generally initially controlled primarily with a proton pump inhibitor, with the addition of an H blocker, or in serious cases, requiring surgical intervention. Diverticulitis and diverticulosis require antibiotic treatment, and may require surgical intervention.

Inflammatory bowel disease is also divided into separate conditions, namely ulcerative colitis and Crohn's disease, which have different medical treatment regimens, and may require surgical intervention in more serious conditions.

Treatment of gastric outlet obstruction depends on the cause, but is usually either surgical or medical.

Treatment is symptomatic, and usually of little value; in most cases, the ulcer heals spontaneously within four to six weeks, sometimes leaving scars. Topical analgesics and anesthetics, as well as topical application of disinfectants/astringents such as potassium permanganate (in sitz baths), is commonly used. In severe cases, a combination of systemic glucocorticoids and broad-spectrum antibiotics has been recommended.

Functional and undifferentiated dyspepsia have similar treatments. Drug therapy decisions are difficult because trials included heartburn in the definition of dyspepsia. This led to the results favoring proton pump inhibitors (PPIs), which are effective for the treatment of heartburn.

Traditional therapies used for this diagnosis include lifestyle modification, antacids, H-receptor antagonists (H2-RAs), prokinetic agents, and antiflatulents. It has been noted that one of the most frustrating aspects of treating functional dyspepsia is that these traditional agents have been shown to have little or no efficacy.

Prior to reaching the advanced stages of colorectal cancer, the polyps are confined to the inner wall and thickness of the intestinal tract and do not metastasize or 'spread'. So provided FAP is detected and controlled either at the pre-cancerous stage or when any cancerous polyps are still internal to the intestinal tract, surgery has a very high success rate of preventing or removing cancer, without recurrence, since the locations giving rise to cancer are physically removed "in toto" by the surgery.

Following surgery, if a partial colectomy has been performed, colonoscopic surveillance of the remaining colon is necessary as the individual still has a risk of developing colon cancer. However, if this happened, it would be a fresh incident from polyps developing anew in the unremoved part of the colon subsequent to surgery, rather than a return or metastasis of any cancer removed by the original surgery.

The drug Elmiron helps, for some patients, to prevent the formation of Hunner's Ulcers by coating the bladder wall, thus making it harder for the acid in urine to irritate the bladder wall lining, which can lead to ulceration. (not cited)

Treatments involve antibiotics that cover for "Pseudomonas aeruginosa". Antipseudomonal penicillins, aminoglycosides, fluoroquinolones, third generation cephalosporins or aztreonam can be given. Usually, the antibiotics are changed according to the culture and sensitivity result. In patients with very low white blood cell counts, Granulocyte-macrophage colony-stimulating factor may be given. Depending on the causal agents, antivirals or antifungals can be added.

Surgery will be needed if there is extensive necrosis not responding to medical treatments.