Treatment can be medical or surgical. Laser endoscopic treatment is often preferred. Voice therapy is sometimes necessary.

In order to prevent further cysts and infections from forming, the thyroglossal duct and all of its branches are removed from the throat and neck area. A procedure, known as the Sistrunk procedure, is considered to be the standard procedure and involves removal of portions of the hyoid bone and core tissue of the suprahyoid region. Cysts will often reoccur if the entire duct is not removed, so reoccurrence requires a wider range of tissue to be removed in a subsequent surgery.

Delaying the surgical procedure almost always leads to recurrent infections, which will continue to delay the needed treatment. The Sistrunk procedure has a reoccurrence rate of less than 5%, proving it is extremely effective at removing the majority of traces of the persistent thyroglossal duct.

Courses of treatment typically include the following:

- Draining the pus once awhile as it can build up a strong odor

- Antibiotics when infection occurs.

- Surgical excision is indicated with recurrent fistular infections, preferably after significant healing of the infection. In case of a persistent infection, infection drainage is performed during the excision operation. The operation is generally performed by an appropriately trained specialist surgeon e.g. an otolaryngologist or a specialist General Surgeon.

- The fistula can be excised as a cosmetic operation even though no infection appeared. The procedure is considered an elective operation in the absence of any associated complications.

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 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.

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.

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.

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.

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.

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.

Most arachnoid cysts are asymptomatic and do not require treatment. Treatment may be necessary when symptomatic. A variety of procedures may be used to decompress (remove pressure from) the cyst.

- Surgical placement of a cerebral shunt:

- An internal shunt drains into the subdural compartment.

- A cystoperitoneal shunt drains to the peritoneal cavity.

- Craniotomy with excision

- Various endoscopic techniques are proving effective, including laser-assisted techniques.

- Drainage by needle aspiration or burr hole.

- Capsular resection

- Pharmacological treatments may address specific symptoms such as seizures or pain.

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.

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.

The cysts can be removed via , though conventional cyst excision techniques have proven impractical, and a specialized regimen is required.

As of 2014 there was no cure for laryngeal papillomatosis, and treatment options aimed to remove and limit the recurrence of the papillomas. Repeated treatments are often needed because of the recurrent nature of the virus, especially for children, as the juvenile form of laryngeal papillomatosis often triggers more aggressive relapses than the adult form. Between recurrences, voice therapy may be used to restore or maintain the persons's voice function.

The primary treatment for urethral diverticulum is surgical. The surgery is conducted transvaginally, usually when there is no acute inflammation to better aid dissection of the delicate tissues.

Treatment for dermoid cyst is complete surgical removal, preferably in one piece and without any spillage of cyst contents. Marsupialization, a surgical technique often used to treat pilonidal cyst, is inappropriate for dermoid cyst due to the risk of malignancy.

The association of dermoid cysts with pregnancy has been increasingly reported. They usually present the dilemma of weighing the risks of surgery and anesthesia versus the risks of untreated adnexal mass. Most references state that it is more feasible to treat bilateral dermoid cysts of the ovaries discovered during pregnancy if they grow beyond 6 cm in diameter.

The first line of treatment is surgery to remove papillomas. Surgery does not prevent recurrences, and can lead to a number of serious complications. Laser technology, and carbon dioxide laser surgery in particular, has been used since the 1970s for the removal of papillomas; however, laser surgery is not without its risks, and has been associated with a higher occurrence of respiratory tract burns, stenosis, severe laryngeal scarring, and tracheoesophagyeal fistulae. Tracheotomies are offered for the most aggressive cases, where multiple debulking surgery failures have led to airways being compromised. The tracheotomies use breathing tubes to reroute air around the affected area, thereby restoring the person's breathing function. Although this intervention is usually temporary, some people must use the tube indefinitely. This method should be avoided if at all possible, since the breathing tube may serve as a conduit for spread of the disease as far down as the tracheobronchal tree.

A microdebrider is a tool that can suction tissue into a blade, which then cuts the tissue. Microdebriders are gradually replacing laser technology as the treatment of choice for laryngeal papillomatosis, due to their ability to selectively suction papillomas while relatively sparing unaffected tissue. In addition to the lower risk of complications, microdebrider surgery also is reportedly less expensive, less time-consuming, and more likely to give the person a better voice quality than the traditional laser surgery approaches.

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.

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.

Most arachnoid cysts are asymptomatic, and do not require treatment. Where complications are present, leaving arachnoid cysts untreated, may cause permanent severe neurological damage due to the progressive expansion of the cyst(s) or hemorrhage (bleeding). However, with treatment most individuals with symptomatic arachnoid cysts do well.

More specific prognoses are listed below:

- Patients with impaired preoperative cognition had postoperative improvement after surgical decompression of the cyst.

- Surgery can resolve psychiatric manifestations in selected cases.

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.

If there is a high probability of a fracture resulting from the unicameral bone cyst, then surgical treatment is necessary. Specific methods can be determined by the physician based upon the patient’s age, medical history, tolerance for certain medical procedures or medicine, health, and extremity of the disease. The treatment can involve or incorporate one or more of the following surgical methods, which are performed by a pediatric orthopedic surgeon:

- Curettage:

- Bone Grafting:

- Steroid injection:

If a patient needs to be treated with surgery, a standard surgical procedure would be called for; the patient would be resting in Fowler’s position, a semi-sitting position, under general anesthesia. The exact size, shape, and distance between the acromion to the midpoint of the cyst are measured by a digital radiograph or MRI scan. A small, longitudinal skin incision, about 1 cm long, is made at the center of the cyst. Next, by using a trephine or drill bit, a small aperture is made inside the incision. Fluids contained in the cyst are drained and curved, metal impactors are used to break any septa, or membranes, within the cyst. Curettes are then used to remove the entire cyst from the diaphysis. After the removal of the cystic membrane, a 95% ethanol solution is injected into the cavity to produce a chemical cauterization to burn away any residual active membrane for 30 seconds and then aspirated. Saline solution is then immediately injected into the cavity to wash out any residual ethanol solution and to mitigate any damage to healthy tissue; this irrigation process of ethanol and saline solutions is repeated for another 2 to 3 times. A curved impactor is inserted into the cavity and used to penetrate the boundary between the cyst and bone marrow; the intentional penetrations will allow bone marrow cells to migrate into the cavity to produce a source of osteoinductive cells, cells that induce bony growth. Furthermore, the cavity is completely filled with bone graft substitute, such as calcium sulfate. Finally, one cannulated screw is placed into the aperture.

In most cases, a fetus with CPAM is closely monitored during pregnancy and the CPAM is removed via surgery after birth. Most babies with a CPAM are born without complication and are monitored during the first few months. Many patients have surgery, typically before their first birthday, because of the risk of recurrent lung infections associated with CPAMs. Some pediatric surgeons can safely remove these lesions using very tiny incisions using minimally invasive surgical techniques (thoracoscopy). However, some CPAM patients live a full life without any complication or incident. It is hypothesized that there are thousands of people living with an undetected CPAM. Through ultrasound testing employed in recent years, many more patients are aware that they live with this condition. Rarely, long standing CPAMs have been reported to become cancerous.

Very large cystic masses might pose a danger during birth because of the airway compression. In this situation, a special surgical type of delivery called the EXIT procedure may be used.

In rare extreme cases, where fetus's heart is in danger, fetal surgery can be performed to remove the CPAM. If non-immune hydrops fetalis develop, there is a near universal mortality of the fetus without intervention. Fetal surgery can improve the chances of survival to 50-60%. Recently, several studies found that a single course of prenatal steroids (betamethasone) may increase survival in hydropic fetuses with microcystic CPAMs to 75-100%. These studies indicate that large microcystic lesions may be treated prenatally without surgical intervention. Large macrocyst lesions may require in utero placement of a Harrison thoracoamniotic shunt.