Surgery is the main treatment for all types of thyroid cancer and is used in nearly every case. If fine needle aspiration (FNA) tests indicate thyroid cancer, or are suspicious for thyroid cancer, the patient will have surgery to remove the tumor and all or part of the remaining benign thyroid gland. Since papillary thyroid cancer is often multifocal (present in both left and right sides of the thyroid gland) and since follicular cancer is more aggressive, most surgeons will remove nearly all of the thyroid gland. This operation is called sub-total or near-total thyroidectomy. Only in the case of papillary cancers smaller than 1 cm (about ½ inch) that show no signs of invasion beyond the thyroid gland, is it likely that the surgeon will perform a lobectomy (remove only the affected side of the thyroid gland). When cancer has spread outside of the thyroid gland, surgery is always used to debulk the tumor (remove as much cancer as possible) that has invaded the neck. This is especially true for treatment of medullary thyroid cancer and anaplastic cancer.

Because thyroid cancer may spread to nearby lymph nodes, these lymph nodes may need to be removed. Sometimes, only one or two enlarged lymph nodes thought to be involved by the cancer are removed. More often, several lymph nodes near the thyroid are removed in an operation called a central compartment neck dissection. Removal of more lymph nodes, including those on the side of the neck is called a modified neck dissection.

The patient is usually given general anesthesia and will be "asleep" during these operations. Patients are usually ready to leave the hospital 1 or 2 days after the operation, if there are no complications. Potential complications of thyroid surgery include temporary or permanent hoarseness or loss of voice (if nerves to the larynx are damaged during surgery), damage to the parathyroid glands (small glands near the thyroid that help regulate blood calcium levels), excessive bleeding, and wound infections. If most of the thyroid gland is removed, the patient will need to take thyroid hormone pills after surgery. Requiring thyroid hormone pills is not a complication—it is intended and is part of the strategy for treating thyroid cancers.