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.

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

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 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.

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.

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.

The infected tissue of the periapical cyst must be entirely removed, including the epithelium of the cyst wall; otherwise a relapse is likely to occur. Root canal treatment should be performed on the tooth if it is determined that previous therapy was unsuccessful. Removal of the necrotic pulp and the inflamed tissue as well as proper sealing of the canals and an appropriately fitting crown will allow the tooth to heal under uninfected conditions.

Surgical options for previously treated teeth that would not benefit from root canal therapy include cystectomy and cystostomy. This route of treatment is recommended upon discovery of the cyst after inadequate root canal treatment. A cystectomy is the removal of a cyst followed by mucosa and wound closure to reduce chances of cyst regeneration. This type of treatment is more ideal for small cysts.

A cystostomy is recommended for larger cysts that compromise important adjacent anatomy. The cyst is tamponaded to allow for the cyst contents to escape the bone. Over time, the cyst decreases in size and bone regenerates in the cavity space.

Marsupialization could also be performed, which involves suturing the edges of the gingiva surrounding the cyst to remain open. The cyst then drains its contents and heal without being prematurely closed. The end result is the same as the cystostomy, bone regeneration. For both a cystostomy and marsupialization, root resectioning may also be required in cases where root resorption has occurred.

The prognosis depends upon the type, size and location of a cyst. Most cysts are entirely benign, and some may require no treatment. Rarely, some cystic lesions represent locally aggressive tumors that may cause destruction of surrounding bone if left untreated. This type of cyst are usually removed with a margin of healthy bone to prevent recurrence of new cysts. If a cyst expands to a very large size, the mandible may be weakened such that a pathologic fracture occurs.

Once a patient with neurocutaneous melanosis becomes symptomatic, little can be done to improve prognosis as there is no effective treatment for the disorder. Most therapies are designed to treat the symptoms associated with the disorder, mainly those related to hydrocephalus. A ventriculoperitoneal shunt to relieve intracranial pressure is the preferred method.

Chemotherapy and radiotherapy have been shown to be ineffective in cases of neurocutaneous melanosis where malignancy is present. Additionally, due to the total infiltration of the central nervous system by these lesions, surgical resection is not a viable treatment option.

It has been demonstrated that early embryonic, post-zygotic somatic mutations in the NRAS gene are implicated in the pathogenesis of NCM. Recently, experimental treatment with MEK162, a MEK inhibitor, has been tried in a patient with NCM and progressive symptomatic leptomeningeal melanocytosis. Pathological studies with immunohistochemical and Western Blot analyses using Ki67 and pERK antibodies showed a potential effect of MEK inhibiting therapy. Further studies are needed to determine whether MEK inhibitors can effectively target NRAS-mutated symptomatic NCM.

The treatment for hemangioblastoma is surgical excision of the tumor. Although usually straightforward to carry out, recurrence of the tumor or more tumors at a different site develop in approximately 20% of patients. Gamma Knife Radiosurgery as well as LINAC have also been employed to successfully treat recurrence and control tumor growth of cerebellar hemangioblastomas.

Choledochal cysts are treated by surgical excision of the cyst with the formation of a roux-en-Y anastomosis hepaticojujenostomy/ choledochojujenostomy to the biliary duct.

Future complications include cholangitis and a 2% risk of malignancy, which may develop in any part of the biliary tree. A recent article published in Journal of Surgery suggested that choledochal cysts could also be treated with single-incision laparoscopic hepaticojejunostomy with comparable results and less scarring. In cases of saccular type of cyst, excision and placement of T-shaped tube is done.

Currently, there is no accepted indication for fetal intervention in the management of prenatally suspected choledochal cysts.

Surgery is not always recommended for syringomyelia patients. For many patients, the main treatment is analgesia. Physicians specializing in pain management can develop a medication and treatment plan to ameliorate pain. Medications to combat any neuropathic pain symptoms such as shooting and stabbing pains (e.g. gabapentin or pregabalin) would be first-line choices. Opiates are usually prescribed for pain for management of this condition. Facet injections are not indicated for treatment of syringomyelia.

Drugs have no curative value as a treatment for syringomyelia. Radiation is used rarely and is of little benefit except in the presence of a tumor. In these cases, it can halt the extension of a cavity and may help to alleviate pain.

In the absence of symptoms, syringomyelia is usually not treated. In addition, a physician may recommend not treating the condition in patients of advanced age or in cases where there is no progression of symptoms. Whether treated or not, many patients will be told to avoid activities that involve straining.

Since the natural history of syringomyelia is poorly understood, a conservative approach may be recommended. When surgery is not yet advised, patients should be carefully monitored. Periodic MRI's and physical evaluations should be scheduled at the recommendation of a qualified physician.

Subcutaneous cysts may be surgically opened to remove less mature bots. If more matured, cysts may be opened and "cuterebra" may be removed using mosquito forceps. Covering the pore in petroleum jelly may aide in removal. If larvae are discovered within body tissues, rather than subcutaneously, surgical removal is the only means of treatment. Ivermectin may be administered with corticosteroids to halt larval migration in cats presenting with respiratory cuterebriasis, but this is not approved for use in cats. There is not yet a known cure for cerebrospinal cuterebriasis.

Because newborns can breathe only through their nose, the main goal of postnatal treatment is to establish a proper airway. Primary surgical treatment of FND can already be performed at the age of 6 months, but most surgeons wait for the children to reach the age of 6 to 8 years. This decision is made because then the neurocranium and orbits have developed to 90% of their eventual form. Furthermore, the dental placement in the jaw has been finalized around this age.

This system is more directly focused on the most appropriate management. These alternatives are broadly to ignore the cyst, schedule follow-up or perform a surgical excision of it. When a cyst shows discrepancy in severity across categories, it is the most worrisome feature that is used in deciding about management. There is no established rule regarding the follow-up frequency, but one possibility is after 6 months, which can later be doubled if unchanged.

Treatment for individuals with Dandy–Walker Syndrome generally consists of treating the associated problems, if needed.

A special tube (shunt) to reduce intracranial pressure may be placed inside the skull to control swelling. Endoscopic third ventriculostomy is also an option.

Treatment may also consist of various therapies such as occupational therapy, physiotherapy, speech therapy or specialized education. Services of a teacher of students with blindness/visual impairment may be helpful if the eyes are affected.

Structural nasal deformities are corrected during or shortly after the facial bipartition surgery. In this procedure, bone grafts are used to reconstruct the nasal bridge. However, a second procedure is often needed after the development of the nose has been finalized (at the age of 14 years or even later).

Secondary rhinoplasty is based mainly on a nasal augmentation, since it has been proven better to add tissue to the nose than to remove tissue. This is caused by the minimal capacity of contraction of the nasal skin after surgery.

In rhinoplasty, the use of autografts (tissue from the same person as the surgery is performed on) is preferred. However, this is often made impossible by the relative damage done by previous surgery. In those cases, bone tissue from the skull or the ribs is used. However, this may give rise to serious complications such as fractures, resorption of the bone, or a flattened nasofacial angle.

To prevent these complications, an implant made out of alloplastic material could be considered. Implants take less surgery time, are limitlessly available and may have more favorable characteristics than autografts. However, possible risks are rejection, infection, migration of the implant, or unpredictable changes in the physical appearance in the long term.

At the age of skeletal maturity, orthognathic surgery may be needed because of the often hypoplastic maxilla. Skeletal maturity is usually reached around the age of 13 to 16. Orthognathic surgery engages in diagnosing and treating disorders of the face and teeth- and jaw position.

Nasopalatine duct cysts usually present as asymptomatic palatal swellings, but they may rarely be accompanied by pain and/or purulent discharge. The cysts are generally treated by .

The first step after diagnosis is finding a neurosurgeon who is experienced in the treatment of syringomyelia. Surgery is the treatment for syringomyelia. Evaluation of the condition is necessary because syringomyelia can remain stationary for long periods of time, and in some cases progress rapidly.

Surgery of the spinal cord has certain characteristic risks associated with it, and the benefits of a surgical procedure on the spine have to be weighed against the possible complications associated with any procedure. Surgical treatment is aimed at correcting the condition that allowed the syrinx to form. It is vital to bear in mind that the drainage of a syrinx does not necessarily mean the elimination of the syrinx-related symptoms but rather is aimed at stopping progression. In cases involving an Arnold-Chiari malformation, the main goal of surgery is to provide more space for the cerebellum at the base of the skull and upper cervical spine without entering the brain or spinal cord. This often results in flattening or disappearance of the primary syrinx or cavity, over time, as the normal flow of cerebrospinal fluid is restored. If a tumor is causing syringomyelia, removal of the tumor is the treatment of choice, if this is considered to be safe.

Surgery results in stabilization or modest improvement in symptoms for most patients. Delay in treatment may result in irreversible spinal cord injury. Recurrence of syringomyelia after surgery may make additional operations necessary; these may not be completely successful over the long term.

In some patients it may also be necessary to drain the syrinx, which can be accomplished using a catheter, drainage tubes, and valves. This system is also known as a shunt. Shunts are used in both the communicating and noncommunicating forms of the disorder. First, the surgeon must locate the syrinx. Then, the shunt is placed into it with the other end draining cerebrospinal fluid (CSF) into a cavity, usually the abdomen. This type of shunt is called a ventriculoperitoneal shunt and is particularly useful in cases involving hydrocephalus. By draining syrinx fluid, a shunt can arrest the progression of symptoms and relieve pain, headache, and tightness. Syringomyelia shunts are not always successful and can become blocked as with other central nervous system shunts.

The decision to use a shunt requires extensive discussion between doctor and patient, as this procedure carries with it greater risk of injury to the spinal cord, infection, blockage, or hemorrhage and may not necessarily work for all patients. Draining the syrinx more quickly does not produce better outcomes, but a shunt may be required if the fluid in the syrinx is otherwise unable to drain.

In the case of trauma-related syringomyelia, the surgeon operates at the level of the initial injury. The syrinx collapses at surgery, but a tube or shunt is usually necessary to prevent re-expansion.

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.

Currently, there is no cure for porencephaly because of the limited resources and knowledge about the neurological disorder. However, several treatment options are available. Treatment may include physical therapy, rehabilitation, medication for seizures or epilepsy, shunt (medical), or neurosurgery (removal of the cyst). According to the location, extent of the lesion, size of cavities, and severity of the disorder, combinations of treatment methods are imposed. In porencephaly patients, patients achieved good seizure control with appropriate drug therapy including valproate, carbamazepine, and clobazam. Also, anti-epileptic drugs served as another positive method of treatment.

Bronchogenic cysts are small, solitary cysts or sinuses, most typically located in the region of the suprasternal notch or over the manubrium.

Autologous stem-cell transplants are shown to be an effective treatment. However, this should be only considered for certain people due to toxicity concerns. It is possible that the transplant may cause problems like septic shock.

Treatment also involves central nervous system penetrating chemotherapy. Options include intrathecal, intraventricular, and systemic chemotherapy. These must penetrate the blood-brain barrier in order to be effective. Sometimes mixing multiple forms of treatment with chemotherapy seems to be the best route. For example, some significant improvement has been shown as a result of cranial radiation treatment preceding a brief course of intrathecal chemotherapy. Although this is an effective treatment to do, penetrating the blood-brain barrier can cause side effects due to the toxicity in the nervous system. These would include dizziness, confusion, and changes in mental status. Another form could be the use of pharmaceuticals, which have all shown positive results for treatment but should always be consulted with a physician to asses risks.

The outcome for hemangioblastoma is very good, if surgical extraction of the tumor can be achieved; excision is possible in most cases and permanent neurologic deficit is uncommon and can be avoided altogether if the tumor is diagnosed and treated early. Persons with VHL syndrome have a bleaker prognosis than those who have sporadic tumors since those with VHL syndrome usually have more than one lesion.