Treatment options for thyroiditis vary, depending on the type of thyroiditis involved and the condition it has caused in a patient's body. Medications are often used to treat thyroiditis. Thyroid hormone replacement medications may be given to patients who experience hypothyroidism. Medication may be taken for between six months and a year before the dosage is gradually lessened to monitor whether a patient requires continued treatment.

Beta blockers, a type of antihypertensive, may be given to patients who have high levels of thyroid hormones in their bloodstream (thyrotoxicosis). These medications, typically used to control high blood pressure, may relieve certain symptoms of hyperthyroidism (e.g., heart palpitations, tremors and shakes) that may accompany thyrotoxicosis. Patients usually need to use these medications for only a short period of time until symptoms go away.

Patients who experience pain of the thyroid gland can usually treat their symptoms with a mild over-the-counter anti-inflammatory medication. Patients with more significant pain may require prescription corticosteroids. Patients are urged not to take any medication without first consulting a physician. Possible risks of long-term use of corticosteroids include diabetes, osteoporosis, glaucoma and cataracts.

In many cases, patients who are diagnosed with thyroiditis require regular follow-up screenings so that a physician can monitor the health of their thyroid gland.

It is not known how to prevent autoimmune disorders, which cause most cases of thyroiditis. In cases where a patient's thyroiditis has a preventable cause, taking appropriate actions to prevent the cause may also prevent thyroiditis. For example, thyroiditis caused by the use of certain medications or treatments may be prevented by using alternative medications or treatments if possible. Taking steps to prevent viral or bacterial infections may also prevent some types of thyroiditis. Recent but as-yet-unconfirmed research suggests that supplementation with selenium may reduce the occurrence of certain types of thyroiditis.