Pain associated with ovarian cysts may be treated in several ways:

- Pain relievers such as acetaminophen, nonsteroidal anti-inflammatory drugs, or opioids.

- While hormonal birth control prevents the development of new cysts in those who frequently get them, it is not useful for the treatment of current cysts.

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.

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.

Although most cases of ovarian cysts involve monitoring, some cases require surgery. This may involve removing the cyst, or one or both ovaries. Technique is typically laparoscopic, unless the cyst is particularly large, or if pre-operative imaging suggests malignancy or complex anatomy. In certain situations, the cyst is entirely removed, while with cysts with low recurrence risk, younger patients, or which are in anatomically eloquent areas of the pelvis, they can be drained. Features that may indicate the need for surgery include:

- Persistent complex ovarian cysts

- Persistent cysts that are causing symptoms

- Complex ovarian cysts larger than 5 cm

- Simple ovarian cysts larger 10 cm or larger than 5 cm in postmenopausal patients

- Women who are menopausal or perimenopausal

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

Breast cysts do not require treatment unless a cyst is large and painful or otherwise uncomfortable. In that case, draining the fluid from a breast cyst can ease symptoms.

Typical treatment involves a Needle aspiration biopsy. Aspirated cysts often recur (come back); definitive treatment may require surgery.

Draining the fluid and then waiting for the cyst to resolve is the main treatment applied in these cases. Moreover, if cysts are aspirated and the fluid looks normal, they do not require any other medical attention apart from following-up to make sure they have completely disappeared. Hormone therapy, by the means of oral contraceptives, is sometimes prescribed to reduce their recurrence and to regulate the menstrual cycle of the patient (which is likely to cause them in the first place). Danazol may also be prescribed to treat this condition and it is usually considered in patients on whom the non-medical treatment fails and the symptoms are intense.

Surgical removal of a breast cyst is necessary only in a few unusual circumstances. If an uncomfortable breast cyst recurs month after month, or if a breast cyst contains blood-tinged fluid and displays other worrisome signs, surgery may be considered.

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.

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.

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.

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.

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.

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.

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.

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.

The development of breast cysts may be prevented to some degree, according to the majority of the specialists. The recommended measures one is able to take in order to avoid the formation of the cysts include practicing good health and avoiding certain medications, eating a balanced diet, taking necessary vitamins and supplements, getting exercise, and avoiding stress.

Although caffeine consumption does not have a scientifically proved connection with the process of cyst development, many women claim that their symptoms are relieved if avoiding it. Some doctors recommend reducing the amount of caffeine in one's diet in terms of both beverages and foods (such as chocolate). Also reducing salt intake may help in alleviating the symptoms of breast cysts, although, again, there is no scientific linkage between these two. Excessive sugar consumption as well as undetected food allergies, such as to gluten or lactose, may also contribute to cyst development.

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 clinical management of a cyst of Montgomery depends upon the symptoms of the patient.

If there are no signs of infection, a cyst of Montgomery can be observed, because more than 80% resolve spontaneously, over only a few months. However, in some cases, spontaneous resolution may take up two years. In such cases, a repeat ultrasonography may become necessary. If, however, the patient has signs of an infection, for example reddening (erythema), warmth, pain and tenderness, a treatment for mastitis can be initiated, which may include antibiotics and non-steroidal anti-inflammatory drugs (NSAIDs). With treatment, inflammatory changes usually disappear quickly. In rare cases, drainage may become necessary. A surgical treatment of a cyst of Montgomery, i.e. a resection, may become necessary only if a cyst of Montgomery persists, or the diagnosis is questioned clinically.

The prognosis seems to be excellent. In one series, all adolescent patients with a cyst of Montgomery had a favourable outcome.

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.

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.

For malignant teratomas, usually, surgery is followed by chemotherapy.

Teratomas that are in surgically inaccessible locations, or are very complex, or are likely to be malignant (due to late discovery and/or treatment) sometimes are treated first with chemotherapy.

Complications of treatment may include joint stiffness and scar formation. Recurrence of the lesion is more common following excision of a volar ganglion cyst in the wrist. Incomplete excision that fails to include the stalk or pedicle also may lead to recurrence, as will failing to execute a layered closure of the incision.

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 fertility drug clomiphene citrate (Clomid, Serophene), used to induce ovulation, increases the risk of a corpus luteum cyst developing after ovulation. These cysts don't prevent or threaten a resulting pregnancy. Women on birth control pills usually do not form these cysts; in fact, preventing these cysts is one way birth control pills work.

In contrast, the progesterone-only pill can cause increased frequency of these cysts.