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.

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.

Radicular cysts are by far the most common cyst occurring in the jaws.

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.

The standard treatment of COC is enucleation and curettage (E&C). Recurrence following E&C is rare.

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.

Botryoid odontogenic cyst is a variant of the lateral periodontal cyst. It is more often found in middle-aged and older adults, and the teeth more likely affected are mandibular (lower) canines and premolars. On radiographs, the cyst appears "grape-like". Often patients with this condition are symptomatic.

Gingival cyst (or dental lamina cyst) is a type of cysts of the jaws that originates from the dental lamina and is found in the mouth parts. It is a superficial cyst in the alveolar mucosa. It can be seen inside the mouth as small and whistish bulge. Depending on the ages in which they develop, the cysts are classsfied into gingival cyst of newborn (or infant) and gingival cyst of adult. Structurally, the cyst is lined by thin epithelium and shows a lumen usually filled with desquamated keratin, occasionally containing inflammatory cells. The nodes are formes as a result of cystic degeneration of epithelial rests of the dental lamina (called the rests of Serres).

Gingival cyst was first described by a Czech physician Alois Epstein in 1880. In 1886, a German physician Heinrich Bohn described another type of cyst. Alfred Fromm introduced the classification of gingival cysts in 1967. According to him, gingival cysts of newborns can be further classsified based on their specific origin of the tissues as Epstein’s pearls, Bohn’s nodules and dental lamina cysts.

Small unilocular lesions have been successfully treated with enucleation and curettage followed by chemical bone cautery. Multilocular tumors exhibit a 25% recurrence rate and, therefore, must be treated more aggressively. In the case of a multilocular myxoma, resection of the tumor with a generous portion of surrounding bone is required. Because of the gelatinous nature of the tumor, it is crucial for the surgeon to remove the lesion intact so as to further reduce the risk of recurrence.

Surgical excision of the lesion is done, and depending upon the clinical circumstances, this may or may not involve removal of the involved tooth. With incomplete removal, recurrence is common; some surgeons advocate curettage after extraction of teeth to decrease the overall rate of recurrence.

Stafne defect is uncommon, and has been reported to develop anywhere between the ages of 11 and 30 years old, (although the defect is developmental, it does not seem to be present form birth, implying that the lesion develops at a later age). Usually the defect is unilateral (on one side only) and most commonly occurs in men.

The lateral periodontal cyst is a non-inflammatory developmental cyst that arises from the epithelial post-functional dental lamina, which is a remnant from odontogenesis. It is more common in middle-aged males. Usually asymptomatic, it presents as a regular well-corticated radiolucency on the side of a mandibular canine or premolar root. Histologically, the cyst appears similar to the gingival cyst of the adult, having a non-keratinized squamous epithelial lining. The involved tooth is usually vital and has no indication for root canal treatment unless the signs of non-vital or necrotic pulpal tissue were confirmed. The cysts arise from epithelial rest cells in the periodontal ligament, although it is unknown whether from the cell rests of Malassez, reduced enamel epithelium or dental lamina remnants, and are generally treated by surgical enucleation.

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.

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 adenomatoid odontogenic tumor is an odontogenic tumor arising from the enamel organ or dental lamina.

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.

Odontogenic cyst are a group of jaw cysts that are formed from tissues involved in odontogenesis (tooth development). Odontogenic cysts are closed sacs, and have a distinct membrane derived from rests of odontogenic epithelium. It may contain air, fluids, or semi-solid material. Intra-bony cysts are most common in the jaws, because the mandible and maxilla are the only bones with epithelial components. That odontogenic epithelium is critical in normal tooth development. However, epithelial rests may be the origin for the cyst lining later.

Not all oral cysts are odontogenic cyst. For example, mucous cyst of the oral mucosa and nasolabial duct cyst are not of odontogenic origin.

In addition, there are several conditions with so-called (radiographic) 'pseudocystic appearance' in jaws; ranging from anatomic variants such as Stafne static bone cyst, to the aggressive aneurysmal bone cyst.

As the condition is quite rare, opinions among experts about how to treat OKCs differ.

Treatment options:

- Wide (local) surgical excision.

- Marsupialization - the surgical opening of the (OKC) cavity and a creation of a marsupial-like pouch, so that the cavity is in contact with the outside for an extended period, e.g. three months.

- Curettage (simple excision & scrape-out of cavity).

- Peripheral ostectomy after curettage and/or enucleation.

- Simple excision.

- Carnoy's solution - usually used in conjunction with excision.

- Enucleation and cryotherapy

It is fairly uncommon, but It is seen more in young people. Two thirds of the cases are found in females.

The calcifying odotogenic cyst or the Gorlin cyst, now known in the WHO Classification of Tumours as the calcifying cystic odontogenic tumor, is a benign odontogenic tumor of cystic type most likely to affect the anterior areas of the jaws. It is most common in people in their second to third decades but can be seen at almost any age. On radiographs, the calcifying odontogenic cyst appears as a unilocular radiolucency (dark area). In one-third of cases, an impacted tooth is involved. Microscopically, there are many cells that are described as "ghost cells", enlarged eosinophilic epithelial cells without nuclei.

The periapical cyst (also termed radicular cyst or inflammatory cyst) is the most common odontogenic cyst. Periapical is defined as "the tissues surrounding the apex of the root of a tooth" and a cyst is "a pathological cavity lined by epithelium, having fluid or gaseous content that is not created by the accumulation of pus." Most frequently located in the maxillary anterior region, it is caused by pulpal necrosis secondary to dental caries or trauma. The cyst has lining that is derived from the epithelial cell rests of Malassez which proliferate to form the cyst. Highly common in the oral cavity, the periapical cyst is asymptomatic, but highly significant because a secondary infection can cause pain and damage. In radiographs, it appears a radiolucency (dark area) around the apex of a tooth's root.

The treatment for CGCG is thorough curettage. A referral is made to an oral surgeon. Recurrence ranges from 15%–20%. In aggressive tumors, three alternatives to surgery are undergoing investigation:

- corticosteroids;

- calcitonin (salmon calcitonin);

- interferon α-2a.

These therapeutic approaches provide positive possible alternatives for large lesions. The long term prognosis of giant-cell granulomas is good and metastases do not develop.

The botryoid odontogenic cyst is a multi-compartmentalized variant of the lateral periodontal cyst. It is similar to the lateral periodontal cyst in all its features except that its polycystic nature is often evident through its multilocular pattern on radiographs.

Gingival cyst of adult is a rare condition. The incidence is less than 0.5%. It is formed from the rests of dental lamina. It is found in the soft tissues on the buccal and labial portions of the jaw. It usually occurs on the facial gingiva as a single small flesh colored swelling, sometimes with a bluish hue due to the cystic fluid. Sometimes, it may occur in cluster, either unilaterally or bilaterally or on the lingual surface of the alveolar process. It is most commonly seen in the canine and premolar regions of the mandible, and are sometimes confused with lateral periodontal cysts. It is not normally problematic, but when it grows larger, it can cause some discomfort. It can be removed by simple surgical excision. They are developed late in life, generally up to the sixth decade of age.

Although the treatment of the cyst was previously enuclation of the cyst with removal of the involved tooth or enuclation with root-canal treatment, the current management is enuclation with the preservation of the involved tooth. However, recent evidence suggests self-resolution of this type of cyst, thus close observation with meticulous oral hygiene measures can be employed unless the cyst is infected and symptomatic.