If small and asymptomatic, no treatment is necessary. Larger, symptomatic cases of Zenker's diverticulum have been traditionally treated by neck surgery to resect the diverticulum and incise the cricopharyngeus muscle. However, in recent times non-surgical endoscopic techniques have gained more importance (as they allow for much faster recovery), and the currently preferred treatment is endoscopic stapling (i.e. diverticulotomy with staples ). This may be performed through a diverticuloscope. Other methods include fibreoptic diverticular repair.

Other non-surgical treatment modalities also exist, such as endoscopic laser, which recent evidence suggests is less effective than stapling.

Although generally benign, the cyst must be removed if the patient exhibits difficulty in breathing or swallowing, or if the cyst is infected. Even if these symptoms are not present, the cyst may be removed to eliminate the chance of infection or development of a carcinoma, or for cosmetic reasons if there is unsightly protrusion from the neck.

Thyroid scans and thyroid function studies are ordered preoperatively; this is important to demonstrate that normally functioning thyroid tissue is in its usual area.

Surgical management options include the Sistrunk procedure, en bloc central neck dissection, suture-guided transhyoid pharyngotomy, and Koempel's supra-hyoid technique. Cystectomy is an inadequate approach.

A neurosurgeon performs a same day surgery to insert an endoscope, which drains the cyst internally.

Treatment is often largely dependent on the type of cyst. Asymptomatic cysts, termed pseudocysts, normally require active monitoring with periodic scans for future growth. Symptomatic (producing or showing symptoms) cysts may require surgical removal if they are present in areas where brain damage is unavoidable, or if they produce chronic symptoms disruptive to the quality of life of the patient. Some examples of cyst removal procedures include: permanent drainage, fenestration, and endoscopic cyst fenestration.

Asymptomatic Schatzki rings seldom worsen over time, and need no treatment.

Symptomatic Schatzki rings may be treated with esophageal dilatation, using bougie or balloon dilators. These have been found to be equally effective. Bougie dilatation involves passage of long dilating tubes of increasing size down the esophagus to stretch the area of narrowing, either over a guidewire passed into the stomach by endoscopy (the "Savary-Gillard" system) or using mercury-weighted dilators (the "Maloney" system). This is usually done with intravenous sedation to reduce discomfort. Dilatation can produce some temporary irritation. A short course of proton pump inhibitor therapy may decrease aggravation by stomach acid reflux into the esophagus. The duration of the benefit of dilation varies, but may be from months to years. Dilation may be repeated if narrowing recurs.

The Sistrunk procedure is the surgical resection of the central portion of the hyoid bone along with a wide core of tissue from the midline area between the hyoid and foramen cecum. It involves excision not only of the cyst but also of the path's tract and branches, and removal of the central portion of the hyoid bone is indicated to ensure complete removal of the tract. The original Sistrunk papers (the "classic" procedure described in 1920, and the "modified" procedure described in 1928) are available on-line with a modern commentary.

In general, the procedure consists of three steps:

1. incision

2. resection of cyst and hyoid bone

3. drainage and closure

There are several versions of the Sistrunk procedure, including:

- "classic": excision of the center of the hyoid bone along with a thyroglossal duct cyst, removal of one-eighth inch diameter core of tongue muscle superior to the hyoid at a 45 degree angle up to the foramen cecum to include mucosa, removal of one-quarter inch of the center of the hyoid bone, closure of the cut ends of the hyoid bone, and placement of a drain.

- modified: dissection through the tongue base but not through the mucosa. The modified Sistrunk procedure is the procedure of choice in both primary and revision cases.

- hyoid cartilage division: In cases without mature ossification of the hyoid bone, the non-fused cartilage portion can be divided by monopolar Bovie electro-cauterization or scissors. There were no statistical differences between this modified Sistrunk and the conventional Sistrunk procedure.

The procedure is relatively safe. In a study of 35 pediatric patients, Maddalozzo et. al found no major complications, but did observe minor complications (6 patients presented with seroma and 4 patients with local wound infections). A more recent paper analyzed 24 research studies on different treatment complications of thyroglossal cyst, and reported a total minor complications rate of 6% for the Sistrunk operation (classical or modified) and simple cystectomy treatment modalities. The Sistrunk procedure also showed better outcomes concerning the rate of overall recurrence, i.e. has the lowest rate of recurrence.

Sistrunk procedure results in a 95% cure rate and 95–100% long-term survival.

If it is caused by esophagitis, in turn caused by an underlying infection, it is commonly treated by treating the infection (typically with antibiotics). In order to open the stricture, a surgeon can insert a bougie – a weighted tube used to dilate the constricted areas in the esophagus. It can sometimes be treated with other medications. For example, an H2 antagonist (e.g. ranitidine) or a proton-pump inhibitor (e.g. omeprazole) can treat underlying acid reflux disease.

Treatment may not be necessary when Bartholin's cysts cause no symptoms. Small, asymptomatic cysts should simply be observed over time to see whether they grow. In cases that require intervention, a catheter may be placed to drain the cyst, or the cyst may be surgically opened to create a permanent pouch (marsupialization). Intervention has a success rate of 85%, regardless of the method used, for the achievement of absence of swelling and discomfort and the appearance of a freely draining duct.

Catheterization is a minor procedure that can be performed in an office setting. A small tube with a balloon on the end (known as a Word catheter) may be inserted into the cyst. The balloon is then inflated to keep it in place. The catheter stays in place for 2 to 4 weeks, draining the fluid and causing a normal gland opening to form, after which the catheter is removed. The catheters do not generally impede normal activity, but sexual intercourse is generally abstained from while the catheter is in place.

Cysts may also be opened permanently, a procedure called marsupialization, in which an opening to the gland is formed with stitches to hold the secretion channel open.

If a cyst is infected, it may break open and start to heal on its own after 3 to 4 days. Nonprescription pain medication such as ibuprofen relieves pain, and a sitz bath may increase comfort. Warm compresses can speed healing. If a Bartholin gland abscess comes back several times, the gland and duct can be surgically removed.

Cysts can be removed by excision.

In case of fronto-ethmoidal epidermoid cysts, surgical resection appears to be the mainstay of treatment; however, the extent of resection is dictated by adherence of the tumor capsule to the surrounding vital structures.

Hydrogen peroxide gel (HO) was previously recommended for cyst treatment, particularly those on body piercings. However the gel cannot adequately permeate the cyst and was not found to be effective. Hydrogen peroxide is no longer recommended for wound care by doctors as it can damage the healing tissues.

On body piercings, self treatment with a hot saline soak to help drain the cyst and the use of an antibacterial or medicated talcum powder (Use of talc is no longer recommended due to recently discovered associations with multiple cancers.) to help dry out the bump and reduce bacterial proliferation is generally recommended until medical advice can be obtained. Piercings, however, are more likely to be victims of hypertrophic scarring than a cyst. Cheek piercings seem to be the piercing most prone to cysts due to the possible interruption of saliva ducts.

Surgical excision of a sebaceous cyst is a simple procedure to completely remove the sac and its contents.

There are three general approaches used: traditional wide excision, minimal excision, and punch biopsy excision.

The typical outpatient surgical procedure for cyst removal is to numb the area around the cyst with a local anaesthetic, then to use a scalpel to open the lesion with either a single cut down the center of the swelling, or an oval cut on both sides of the centerpoint. If the cyst is small, it may be lanced instead. The person performing the surgery will squeeze out the keratin surrounding the cyst, then use blunt-headed scissors or another instrument to hold the incision wide open while using fingers or forceps to try to remove the cyst intact. If the cyst can be removed in one piece, the "cure rate" is 100%. If, however, it is fragmented and cannot be entirely recovered, the operator may use curettage (scraping) to remove the remaining exposed fragments, then burn them with an electro-cauterization tool, in an effort to destroy them in place. In such cases the cyst may recur. In either case, the incision is then disinfected and, if necessary, the skin is stitched back together over it. A scar will most likely result.

An infected cyst may require oral antibiotics or other treatment before or after excision. If pus has already formed then incision and drainage should be done along with avulsion of cyst wall with proper antibiotics coverage.

An approach involving incision, rather than excision, has also been proposed.

Various management options exist depending on the severity of symptoms and their effect on the patient. The main management options are: observation, craniotomy for microsurgical resection, neuroendoscopic removal, stereotactic drainage, and cerebrospinal fluid diversion with bilateral ventriculoperitoneal shunting placement.

When treatment is required, this is usually by surgical removal of the cyst. There are four ways in which cysts are managed:

- Enucleation - removal of the entire cyst

- Marsupialization - the creation of a window into the wall of a cyst, allowing the contents to be drained. The window is left open, and the lack of pressure within the cyst causes the lesion to shrink, as the surrounding bone starts to fill in again.

- Enucleation following marsupialization - Sometimes marsupialization is carried out as a single procedure, but usually it is followed by a second procedure to remove the cyst. This is particularly the case when cysts are very large and their removal would leave a significant surgical defect.

- Enucleation with curettage - this is removal of the cyst and some of the surrounding bone, which may contain some of the lining of the cyst.

Esophageal webs and rings can be treated with endoscopic dilation.

Sebaceous cysts generally do not require medical treatment. However, if they continue to grow, they may become unsightly, painful, infected, or all of the above.

Treatment ranges from simple enucleation of the cyst to curettage to resection. For example, small radicular cyst may resolved after successful endodontic ("root-canal") treatment. Because of high recurrence potential and aggressive behaviour, curettage is recommended for keratocyst. However, the conservative enucleation is the treatment of choice for most odontogenic cysts. The removed cyst must be evaluated by pathologist to confirm the diagnosis, and to rule out other neoplastic lesions with similar clinical or radiographic features (e.g., cystic or solid ameloblastoma, central mucoepidermoid carcinoma). There are cysts, e.g. buccal bifurcation cyst with self-resolation nature, in which close observation can be employed unless the cyst is infected and symptomatic.

Treatment ranges from simple enucleation of the cyst to curettage to resection. There are cysts—e.g., buccal bifurcation cyst—that resolve on their own, in which just close observation may be employed, unless it is infected and symptomatic.

The standard treatment of food bolus obstruction is the use of endoscopy or fibre-optic cameras inserted by mouth into the esophagus. Endoscopes can be used to diagnose the cause of the food bolus obstruction, as well as to remove the obstruction. Traditional endoscopic techniques involved the use of an overtube, a plastic tube inserted into the esophagus prior to the removal of the food bolus, in order to reduce the risk of aspiration into the lungs at the time of endoscopy. However, the "push technique", which involves insufflating air into the esophagus, and gently pushing the bolus toward the stomach instead, has emerged as a common and safe way of removing the obstruction.

Other tools may be used to remove food boluses. The Roth Net® is a mesh net that can be inserted through the endoscope, and opened and closed from the outside; it can be used to retrieve pieces of obstructed food. Snares, which are normally used to remove polyps can be used to macerate the food causing the obstruction. Dormia baskets, which are metal baskets used to remove stones from the common bile duct in a procedure known as endoscopic retrograde cholangiopancreatography, can be opened and closed from the outside in a similar manner to macerate food and facilitate removal. Forceps used for biopsies can also be employed in a similar manner.

Multiple studies have been found on how to remove a colloid cyst. One is an endoscopic removal. To remove the cyst, make a small incision. The endoscope is inserted into the brain and then moved toward the tumor in the ventricular compartment. The tumor is hit with an electric current. The interior of the cyst is removed followed by the cyst wall. The electric current is then used to kill the remaining pieces of the cyst. This whole process, including closing of the incision and removal of the scope is completed within 45 minutes to an hour. The patients are able to leave the hospital after 1 or 2 days. A case was done with the absence of ventriculomegaly that has been contraindication in an endoscopic removal. The study found that with normal-sized ventricles are not a contraindication. They actually have comparable or less complication rates. Another study experimented with a smaller retractor tube, 12 mm instead of 16–22 mm. The study found that using a 12 mm tube on a 10 mm colloid cyst. The surgery was successful in removing the cyst with a smaller retractor tube for resection while minimizing injury. The surgery had potential for improving outcomes.

Neuroendoscopic third ventriculostomy during surgery can be used to prevent further hydrocephalus post op. This removes the need for insertion of bilateral shunts.

Besides the frequent choice to leave the cyst in place, surgical treatments remain the primary elective option for treatment of ganglion cysts. The progression of ganglion surgery worldwide is to use an arthroscopic or mini-opening method. Alternatively, a hypodermic needle may be used to drain the fluid from the cyst (via aspiration) and a corticosteroid may be injected after the cyst is empty; however, if the fluid has thickened, owing to the passage of time, this treatment is not always effective.

There is a recurrence rate of approximately 50% following needle drainage (via aspiration) of ganglion cysts.

One common and traditional method of treatment for a ganglion cyst was to strike the lump with a large and heavy book, causing the cyst to rupture and drain into the surrounding tissues. Historically, a Bible was the largest or only book in any given household, and was often employed for this treatment. This led to the former nickname of "Bible bumps" or "Gideon's disease" for these cysts. This treatment risks injuring the patient.

In patients who have no response to medical or endoscopic therapy, surgery can be performed. A Heller myotomy involves an incision to disrupt the LES and the myenteric plexus that innervates it. The Heller myotomy is used as a final treatment option in patients who do not respond to other therapies.

Pancreatic pseudocyst treatment should be aimed at avoiding any complication (1 in 10 cases become infected). They also tend to rupture, and have shown that larger cysts have a higher likelihood to become more symptomatic, even needing surgery. If no signs of infection are present, initial treatment can include conservative measures such as bowel rest (NPO), parenteral nutrition (TPN), and observation. Serum amylase levels can be trended. If symptoms do not improve by 6 weeks, surgical intervention may be appropriate.

In the event of surgery:

- Cystogastrostomy: In this surgical procedure a connection is created between the back wall of the stomach and the cyst such that the cyst drains into the stomach.

- Cystjejunostomy: In this procedure a connection is created between the cyst and the small intestine so that the cyst fluid directly into the small intestine.

- Cystduodenostomy: In this procedure a connection is created between the duodenum (the first part of the intestine) and the cyst to allow drainage of the cyst content into duodenum. The type of surgical procedure depends on the location of the cyst. For pseudocysts that occur in the head of the pancreas a cystduodenostomy is usually performed.

Both before and after treatment, achalasia patients may need to eat slowly, chew very well, drink plenty of water with meals, and avoid eating near bedtime. Raising the head off the bed or sleeping with a wedge pillow promotes emptying of the esophagus by gravity. After surgery or pneumatic dilatation, proton pump inhibitors are required to prevent reflux damage by inhibiting gastric acid secretion, and foods that can aggravate reflux, including ketchup, citrus, chocolate, alcohol, and caffeine, may need to be avoided.

Treatment may include antibiotic therapy, hot compresses and application of depilatory creams. In more severe cases, the cyst may need to be lanced or treated surgically. Lancing is performed using a local anesthesia, with healing time generally under one week. The most conservative surgical treatment, Bascom's Pit Picking procedure, is a relatively simple outpatient option that can be performed in a physician's office, involves minimal pain and requires only a few days healing. Although this procedure is much less invasive than the alternatives, it is not regularly practiced in the US. The Pit Picking procedure provides good results, fast recovery, and in instances where it is unsuccessful, other options for more invasive surgery can still be performed.

The more common course for surgical treatment is for the cyst to be surgically excised (along with pilonidal sinus tracts). Post-surgical wound packing may be necessary, and packing typically must be replaced once daily for 4 to 8 weeks. In some cases, two years may be required for complete granulation to occur. Sometimes the cyst is resolved via surgical marsupialization.

Surgeons can also excise the sinus and repair with a reconstructive flap technique, such as a "cleft lift" procedure or Z-plasty, usually done under general anesthetic. This approach is especially useful for complicated or recurring pilonidal disease, leaves little scar tissue and flattens the region between the buttocks, reducing the risk of recurrence. This approach typically results in a more rapid recovery than the traditional surgery, however there are fewer surgeons trained in the cleft lift procedure and thus, it may not be as accessible to patients, depending on their geographic location. Meta analysis shows recurrence rates were lower in open healing than with primary closure (RR 0.60, 95% CI 0.42 to 0.87) at the expense of time to healing. Pilonidal cysts recur and do so more frequently if the surgical wound is sutured in the midline, as opposed to away from the midline, which obliterates the natal cleft and removes the focus of shearing stress. An incision lateral to the intergluteal cleft is therefore preferred, especially given the poor healing of midline incisions in this region.

An attractive minimally invasive technique is to treat pilonidal sinus with fibrin glue. This technique is less painful than traditional excisional techniques and flaps, can be performed under local or general anaesthesia, does not require dressings or packing and allows return to normal activities within 1 to 2 days. Long term outcome and recurrence rates are not dissimilar to more invasive techniques in 5 year follow up in a small randomised controlled trial.

Fibrin glue has also been shown to be better than more invasive alternatives in the treatment of pilonidal sinus disease in children, where a quick return to normal activities and minimal postoperative pain are especially important.

A minimally invasive surgical technique, was developed in Israel by Moshe Gips et al.,2008. and is similar to the pit picking technique first described by Bascom in 1980 In this procedure, trephines or biopsy punches which only "core out" and remove the diseased tissue and cyst are used, leaving only small holes to heal. Work or school activities will be resumed in one or two days, without or with minimal postoperative pain. The two procedures have been successfully combined by L. Basso in Rome (Italy).

While the recovery rate is positive for most, some suffer long term effects. Recorded instances include patients with continued postoperative pain for years following the surgical procedure. Primary complaints included pain when sitting for long period of times or following abrasive contact with the lower back and buttocks.

Surgical excision is required to treat a trichilemmal cyst. The method of treatment varies depending on the physician's training. Most physicians perform the procedure under local anesthetic. Others prefer a more conservative approach. This involves the use of a small punch biopsy about 1/4 the diameter of the cyst. The punch biopsy is used to enter the cyst cavity. The content of the cyst is emptied, leaving an empty sac. As the pilar cyst wall is the thickest and most durable of the many varieties of cysts, it can be grabbed with forceps and pulled out of the small incision. This method is best performed on cysts larger than a pea which have formed a thick enough wall to be easily identified after the sac is emptied. Small cysts have walls that are thin, and easily fragmented on traction. This increases the likelihood of cyst recurrence. This method often results in only a small scar, and very little if any bleeding.

Drugs that reduce LES pressure are useful. These include calcium channel blockers such as nifedipine and nitrates such as isosorbide dinitrate and nitroglycerin. However, many patients experience unpleasant side effects such as headache and swollen feet, and these drugs often stop helping after several months.

Botulinum toxin (Botox) may be injected into the lower esophageal sphincter to paralyze the muscles holding it shut. As in the case of cosmetic Botox, the effect is only temporary and lasts about 6 months. Botox injections cause scarring in the sphincter which may increase the difficulty of later Heller myotomy. This therapy is recommended only for patients who cannot risk surgery, such as elderly people in poor health. Pneumatic dilatation has a better long term effectiveness than botox.